LOCUS       CP086649                4686 bp    DNA     circular BCT 17-APR-2024
DEFINITION  Enterococcus faecium strain 2001564 plasmid p2001564_5, complete
            sequence.
ACCESSION   CP086649
VERSION     CP086649.1
DBLINK      BioProject: PRJNA573902
            BioSample: SAMN22929416
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4686)
  AUTHORS   Gargis,A. and Kent,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-NOV-2021) Division of Healthcare Quality Promotion,
            CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2021
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 159.84x
            Sequencing Technology :: Oxford Nanopore and Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 11/12/2021 13:04:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.3
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,072
            CDSs (total)                      :: 2,981
            Genes (coding)                    :: 2,887
            CDSs (with protein)               :: 2,887
            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)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 33 of 94
            Pseudo Genes (incomplete)         :: 61 of 94
            Pseudo Genes (internal stop)      :: 16 of 94
            Pseudo Genes (multiple problems)  :: 13 of 94
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4686
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2001564"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2001564_5"
                     /geo_loc_name="USA"
                     /collection_date="2019"
     gene            join(4651..4686,1..888)
                     /locus_tag="LOE01_15340"
     CDS             join(4651..4686,1..888)
                     /locus_tag="LOE01_15340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WZK08826.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            904..1443
                     /locus_tag="LOE01_15345"
     CDS             904..1443
                     /locus_tag="LOE01_15345"
                     /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="WZK08827.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            2128..2301
                     /locus_tag="LOE01_15350"
     CDS             2128..2301
                     /locus_tag="LOE01_15350"
                     /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="WZK08828.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNGELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            2752..3285
                     /locus_tag="LOE01_15355"
     CDS             2752..3285
                     /locus_tag="LOE01_15355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WZK08824.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     gene            3297..3500
                     /locus_tag="LOE01_15360"
     CDS             3297..3500
                     /locus_tag="LOE01_15360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002307460.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WZK08825.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     Typing          2..888
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatcatattc ctctgagaaa atttaatagt cgtgaaatga acttattttt ttcaattgct
       61 tcacgtgtac gtgaaaaagg tgtagatgag attatttttt catttcacga tttgaaaaaa
      121 ctaagcggtt atacagaacg tggggaacaa tttataaaag atcttagtag cacgtatgac
      181 aaattattaa gtattaatgc ttggaatgat gatggaaata ctttaactaa atttgttgct
      241 ttcacaaaat atagcattat acgagataaa caacttgtta taatttcagt taatccagaa
      301 tttaaaggac tttttaatca attaaagaac tggacaagat ttaatctaga gcaatttact
      361 aatttggata gcacatattc aaaaactatg tttcgattat taaaacaata tcgaactcaa
      421 ggctggactg aattttccaa agaaaaattt tttgatttac tagatattcc taaaagttat
      481 tggaatagtc cgtcaaatat tgacaaattt atcttaaggc caattaaaga agaactcact
      541 cccttattta aaggattaac tattcgtaaa aaatatggta aaggtcgagg taaacctgtt
      601 atcggttatc gttttacttg gaaagctgaa attaaccatg ctgacgattt ttccaaaggg
      661 aaacaagaag atttacgtat aaaattattt aatattgatc acaatggaga attaacacga
      721 gaagaaaaat ggcgcgctaa agatcgaata ctaaatcttc ccttaggcac tcatgaagct
      781 gattttaaac aacaacaaca aactgaagaa aaacaggcag aaaaacgaga actttcaaac
      841 aaactcaaac aagatttact aggaaattta caaaacttat tcgattaagc ttaaggagta
      901 tttatggcag ataaaacaat caaagaactt gcggaagaat taggagttag taaaacagca
      961 attaacaaaa aagtttctga caaaaatcga aaactttggt ttgcaaaaaa cggaaacaag
     1021 tttgtgatta acgaaaccgg tcaaaaagct ataaaatcaa tgtttttagt cgataacgca
     1081 aacttaaatc gaaaactagt tggcgaaaaa tcaaaaacca aaaaccataa aaacaccaac
     1141 caagtttccg aattaaaact cctttctttc ctagaaaaac agttaaatcg aaaagatata
     1201 cagctacaag aaaaagataa tcaaataaaa caaatgcaaa aattactcga ccagcaacaa
     1261 caactcactc tacaagcgaa ccaacaaatt gagaacctac aagaacagct ccatttaact
     1321 tatacagaag aaactccaac aaccgaatca actgcctttt ctgaaaaaaa agcagacaat
     1381 acacaaccac ttattgaaaa aaagtggtgg caaatttgga aatctaatag aaccaatctc
     1441 taaaattttc tagaagttag ttcggatagt agaggaaaaa gttgtactac ctgatgggga
     1501 gatcactcaa atttttatga gaaagaaaaa atagtttaca actgtaaaca atcaatgttt
     1561 atagttgtaa actatcaaac tatatggtga cttattgctt aaaataggtt gaaatctcac
     1621 tcaatttttg gtggaaaaac aaaataaatt ctaatcgatt ttgttgaaaa agtcataaaa
     1681 aaacaaatgt gattttaaca aaatttcaaa aaaatcgttt gaaatttcgt ttattttttt
     1741 tgagaatttt gatcatcgta gggtcattgt agaatcatta tgagatcatc gtgggatcat
     1801 cgaataaagt atgggaaagg cttgcggtgc ttggtattaa gggcattctc cgcctcccag
     1861 gttcttgacc attttctctc aacgtggtaa aaatcccact tataagagaa aatggtcaag
     1921 aacctaaacg gtcggcgaag aaaacatacc aagcaccaca agcaaaaaaa gttagagtaa
     1981 cttccaaaaa agaaaaattt tttagaacaa cttttgaaaa tttaattttg atttatatcc
     2041 gttcaattta aacatttgat aaactgaagg ctagtattta aaatgtgtat acaagtggta
     2101 gcgttaaaaa aagtggaggt ataacctatg ttaaaaaaaa ctgtgttggt actgggttct
     2161 atttctctag gaatattagg ttttagcccc atgctattat ccgtaattgg aaaaaacaat
     2221 tccaacggag aacttaaatt aaattcaaat tattacaaca gtcctaacga agaattgttt
     2281 gtaaaagaga cggataaata ataaaaaaga ctgctctttc gagcagccag ttaaaaaata
     2341 atgagtgttt attcttgaaa aagcaacgcg cttatgaagc gctaccaaaa atttatcata
     2401 ttttatgaaa aataacaccc cagtaaaaaa tgactggtaa aaattcacaa agaaacggaa
     2461 agaagcaact gcagaaaatc aagccttaaa aagagctttt gacttagacc aatcgaaaat
     2521 cacaaagtga gcccctgtat cccttggtag agaggctact tggcatagta cacattatgt
     2581 caacaagaat ttaatataac atattttcct aatgcattct aactatacca cattatcaaa
     2641 aatataaatt atctttacta aataaaatat tgacaagcct ataccttttg ttttatgatt
     2701 ttcacaaaga aaacgttttc tatatatttt tctgtatcag gaggaaattc tatgaaaaaa
     2761 tttactttag gggtagcttt gttaactatt ggggcagttg ttttaccgtc aactactata
     2821 gtttatgctt cagaaaattc ccaagtggta tcattaaacg aaaacaatgc tactgaaaat
     2881 gtagttattg agtacactga agatggtatg gtcgtaacta aatatgagga tggttatagt
     2941 gcggaagatt ttgcaaattc ttcagatatc atgacaagag ctgcagttgc aagatggggc
     3001 aaaaaggaat atacaaatat tgctgtaacc actggagtag ctgctaatgc tattaatgct
     3061 gccttttggg caggagggaa agctagcact tctatgtttg gtatcccagg ttgggcaatt
     3121 ggtgctttgt taacaggtgc aagttggact aaaaaaggtg cttctccagg gaatgcagtt
     3181 gcaaaagaat gggacaaaaa tggtaatggc tggattggat tttattacca aaggggatat
     3241 gatgcagctg gaagagttgt agctactaga tattcaacgt tataagttaa ggagtgatgt
     3301 ttttgatatc taaatcatta aaatcattaa aaacatttac taaaaagaat ccgcaaatag
     3361 ctactattcg tatttttata tttgctatag ctgttgctat aattgttaat atgctaagcg
     3421 gagggcaatt atacaaatct ggtttatttt tagtgttaat cttagttgtc ttagacataa
     3481 taaagtctaa aaaaaaataa atcgatacat tttagaagaa tagggttgtt tgaatattac
     3541 aaagcaacaa tttcaccttc ggtgaaataa gcgaaacttt acaaaaagtg gctagcaaat
     3601 gctagccttt ttttgtattg tggagcgtgg attttgaggg ggattcaagg gggagcttgc
     3661 gctcctttga caagcggtta tttgcaccaa atacggaggt atttggctag caaatataga
     3721 gcttgccaaa cccttttagt gagttttgta gaaagtacct ttaaaggtac tttcacatta
     3781 cgaacgatac gtccgtagga cgtactgaaa gggtgggact tatgagcaaa ttaatgcaaa
     3841 atttggctag caaaaaagct aaaaaatata tgctaataat cgagcgaaat aaacactttt
     3901 tcaagtgagc gaatccgcca tgacaaagct gaagcagttt atttcagctt tgtcatggcg
     3961 tgtgccgact tttttaaaag tctaggcaca cgagcaaata tctttatcaa gctctaattt
     4021 gcgttttaag acgtttgaaa cgcctaagta tataaatata taagaatagg tttaagagtg
     4081 cttaaatcga attttagagg gcatttagac aattttaggg ttgttagggc ttgccctgac
     4141 cgcctgtaag gcgttttaag aacaagataa gggatttata ctaggactgt cttaaaatgt
     4201 cttaaacgaa cgctcagagc ttctcaaagg gttccttatg aacggctttt agcaaaggag
     4261 ccggaggcga ctgcgcagta taatgtgaga gcagagcgat cacacctttt tagcgaaccg
     4321 tagggagcaa ggtttggaat tggcagtttt gataaattcg cgaacctgtt tagagaaaaa
     4381 aggagtgatt ttttaggcgg gaaaattagc ctcccctctt tttatatctc tttttatatc
     4441 tctttttata tctcttttat gtcggctgtg tccttactct cccaagcaat tcagagtttt
     4501 ttcaagtagg ttttctacgc ttttcaagta ggttttctac gcttttcaag taggttttct
     4561 acgcttttca agtaggtttt ccgacattat tgagtatttt tataaagtat gttactttta
     4621 tttcatactt tataaaagta ggagaagctt atggcaaatg aaattgtaaa atatgaaaat
     4681 agatta
//
