LOCUS       NZ_CP085915             4463 bp    DNA     circular CON 24-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762-D plasmid p9, complete sequence.
ACCESSION   NZ_CP085915
VERSION     NZ_CP085915.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22627489
            Assembly: GCF_020736625.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4463)
  AUTHORS   Zeng,W.
  TITLE     Acquisition of daptomycin resistance by Enterococcus faecium confers
            collateral sensitivity to glycopeptides
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4463)
  AUTHORS   Zeng,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-OCT-2021) Laboratory Medicine, College of Life
            Sciences, Wenzhou Medical University, Wenzhou Medical University,
            Wenzhou, Zhejiang 325000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/23/2023 20:46:10
            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)                     :: 3,310
            CDSs (total)                      :: 3,219
            Genes (coding)                    :: 3,060
            CDSs (with protein)               :: 3,060
            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)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 63 of 159
            Pseudo Genes (incomplete)         :: 94 of 159
            Pseudo Genes (internal stop)      :: 41 of 159
            Pseudo Genes (multiple problems)  :: 30 of 159
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP085915.1.
            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..4463
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="SC1762-D"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p9"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            join(4453..4463,1..424)
                     /gene="bacA"
                     /locus_tag="LLE91_RS16455"
                     /old_locus_tag="LLE91_16455"
     CDS             join(4453..4463,1..424)
                     /gene="bacA"
                     /locus_tag="LLE91_RS16455"
                     /old_locus_tag="LLE91_16455"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     gene            1716..2639
                     /locus_tag="LLE91_RS16460"
                     /old_locus_tag="LLE91_16460"
     CDS             1716..2639
                     /locus_tag="LLE91_RS16460"
                     /old_locus_tag="LLE91_16460"
                     /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            2655..3194
                     /locus_tag="LLE91_RS16465"
                     /old_locus_tag="LLE91_16465"
     CDS             2655..3194
                     /locus_tag="LLE91_RS16465"
                     /old_locus_tag="LLE91_16465"
                     /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            3875..4048
                     /locus_tag="LLE91_RS16470"
                     /old_locus_tag="LLE91_16470"
     CDS             3875..4048
                     /locus_tag="LLE91_RS16470"
                     /old_locus_tag="LLE91_16470"
                     /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          1717..2639
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattattaaa attattactt gtctattttt gttcggtatg attgttggag caagtactcc
       61 gttaaatctg tttcctttta gtgctagagg tataaaagtg gaagctgcaa gttcacgata
      121 taatcataat catcgtggat ttacttgcta taaaatgaac tattatgtta ctaataaaat
      181 gtgtagagat ttgaaaaaaa attataataa gctaaagact cctgctcaaa ttgcatcttt
      241 tattcctatt ggtggagttg gaacatgggt tattacaaat gcttttagta gtgctgttga
      301 tgcaatgaat gtctttgtaa gagctgcaaa tcaaggaaaa ggtgtacaat taacatataa
      361 tgctcacttt agcaatacaa catcatatca atacaatgat tacgctcgtt atgtaataaa
      421 ataatcagaa agtgaaacta tctcatgaat aaaaagattt tagctgtaat tatttcaata
      481 atagttttaa tcactatgtt cttcatattt aggctaattt tcaatataag cttacaaaaa
      541 agtattcttt atctaattcc tatagcattt atcttagcaa tttttagaag tatttacgga
      601 aataaaaact ctaaatagct aaaaataaat catactaaat tttacaaaaa gtggctagca
      661 ttttctagcc actttttgta ttgtggagcg tgggttttga gggggattca agggggagct
      721 tgcgcccctt tgacaagcgg ttatttgcac caaatacgga ggtatttggc tagcaaatat
      781 agagcttgcc aaaccctttt agtgagtttt gtagaaagta cctttaaagg tactttcaca
      841 ttacgaacga tacgtccgta ggacgtactg aaagggtggg acttatgagc aaattaatgc
      901 aaaatttggc tagcaaaaaa gctaaaaaat atatgctaat aatcgagcga aataaacact
      961 ttttcaagtg agcgaatccg ccatgacaaa gctgaagcag tttatttcag ctttgtcatg
     1021 gcgtgtgccg acttttttaa aagtctaggc acacgagcaa atatctttat caagctctaa
     1081 tttgcgtttt aagacgtttg aaacgcctaa gtatataaat atataagaat aggtttaaga
     1141 gtgcttaaat cgaattttag agggcattta gacaatttta gggttgttag ggcttgccct
     1201 gaccgcctgt aaggcgtttt aagaacaaga taagggattt ttatactagg actgtcttaa
     1261 aatgtcttaa acgaacgctc agagcttctc aaagggttcc ttatgaacgg cttttagcaa
     1321 aggagccgga ggcgactgcg cagtataatg tgagagcaga gcgatcacac ctttttagcg
     1381 aaccgtaggg agcaaggttt ggaattggca gttttgataa attcgcgaac ctgtttagag
     1441 aaaaaaggag tgatttttta ggcgggaaaa ttagcctccc ctctttttat atctcttttt
     1501 atatctcttt ttatatctct tttatgtcgg ctgtgtcctt actctcccaa gcaattcaga
     1561 gttttttcaa gtaggttttc tacgcttttc aagtaggttt tctacgcttt tcaagtaggt
     1621 tttctacgct tttcaagtag gttttccgac attattgagt atttttataa agtatgttac
     1681 ttttatttca tactttataa aagtaggaga agcttatggc aaatgaaatt gtaaaatatg
     1741 aaaatagatt aaatcatatt cctctgagaa aatttaatag tcgtgaaatg aacttatttt
     1801 tttcaattgc ttcacgtgta cgtgaaaaag gtgtagatga gattattttt tcatttcacg
     1861 atttgaaaaa actaagcggt tatacagaac gtggggaaca atttataaaa gatcttagta
     1921 gcacgtatga caaattatta agtattaatg cttggaatga tgatggaaat actttaacta
     1981 aatttgttgc tttcacaaaa tatagcatta tacgagataa acaacttgtt ataatttcag
     2041 ttaatccaga atttaaagga ctttttaatc aattaaagaa ctggacaaga tttaatctag
     2101 agcaatttac taatttggat agcacatatt caaaaactat gtttcgatta ttaaaacaat
     2161 atcgaactca aggctggact gaattttcca aagaaaaatt ttttgattta ctagatattc
     2221 ctaaaagtta ttggaatagt ccgtcaaata ttgacaaatt tatcttaagg ccaattaaag
     2281 aagaactcac tcccttattt aaaggattaa ctattcgtaa aaaatatggt aaaggtcgag
     2341 gtaaacctgt tatcggttat cgttttactt ggaaagctga aattaaccat gctgacgatt
     2401 tttccaaagg gaaacaagaa gatttacgta taaaattatt taatattgat cacaatggag
     2461 aattaacacg agaagaaaaa tggcgcgcta aagatcgaat actaaatctt cccttaggca
     2521 ctcatgaagc tgattttaaa caacaacaac aaactgaaga aaaacaggca gaaaaacgag
     2581 aactttcaaa caaactcaaa caagatttac taggaaattt acaaaactta ttcgattaag
     2641 cttaaggagt atttatggca gataaaacaa tcaaagaact tgcggaagaa ttaggagtta
     2701 gtaaaacagc aattaacaaa aaagtttctg acaaaaatcg aaaactttgg tttgcaaaaa
     2761 acggaaacaa gtttgtgatt aacgaaaccg gtcaaaaagc tataaaatca atgtttttag
     2821 tcgataacgc aaacttaaat cgaaaactag ttggcgaaaa atcaaaaacc aaaaaccata
     2881 aaaacaccaa ccaagtttcc gaattaaaac tcctttcttt cctagaaaaa cagttaaatc
     2941 gaaaagatat acagctacaa gaaaaagata atcaaataaa acaaatgcaa aaattactcg
     3001 accagcaaca acaactcact ctacaagcga accaacaaat tgagaaccta caagaacagc
     3061 tccatttaac ttatacagaa gaaactccaa caaccgaatc aactgccttt tctgaaaaaa
     3121 aagcagacaa tacacaacca cttattgaaa aaaagtggtg gcaaatttgg aaatctaata
     3181 gaaccaatct ctaaaatttt ctagaagtta gttcggatag tagaggaaaa agttgtacta
     3241 cctgatgggg agatcactca aatttttatg agaaagaaaa aatagtttac aactgtaaac
     3301 aatcaatgtt tatagttgta aactatcaaa ctatatggtg acttattgct taaaataggt
     3361 tgaaatctca ctcaattttt ggtggaaaaa caaaataaat tctaatcgat tttgttgaaa
     3421 aagtcataaa aaaacaaatg tgattttaac aaaatttcaa aaaaatcgtt tgaaatttcg
     3481 tttatttttt ttgagaattt tgatcatcgt agggtcattg tagaatcatt atgagatcat
     3541 cgtgggatca tcgaataaag tatgggaaag gcttgcggtg cttggtatta agggcattct
     3601 ccgcctccca ggttcttgac cattttctct tataagtggg atttttacca cgttgagaga
     3661 aaatggtcaa gaacctggga ggcggagaaa acataccaag caccacaagc aaaaaaagtt
     3721 agagtaactt ccaaaaaaga aaaatttttt agaacaactt ttgaaaattt aattttgatt
     3781 tatatccgtt caatttaaac atttgataaa ctgaaggcta gtatttaaaa tgtgtataca
     3841 agtggtagcg ttaaaaaaag tggaggtata acctatgtta aaaaaaactg tgttggtact
     3901 gggttctatt tctctaggaa tattaggttt tagccccatg ctattatccg taattggaaa
     3961 aaacaattcc aacagagaac ttaaattgaa ttcaaattat tacaacagtc ctaacgaaga
     4021 attgtttgta aaagaaacgg ataaataata aaaaagactg ctcttccgag cagccagtta
     4081 aaaaataatg agtgtttatt cttgaaaaag caacgcgctt ataaagcgct accaaaaatt
     4141 tatcatattt tatgaaaaat aacaatccag taaaaaatga ctggtaaaaa ttcacaaaga
     4201 aacggaaaga agcaactgca gaaaatcaag ccttaaaaag agctttttac ctagaccaat
     4261 taaaaatcac aaagtgagcc cctgtatcgg ttgatacaag ggctacttgg catactcgac
     4321 attatgtcta ctaaccttta aaataacacg ttttataaaa taaaccctct tgacaatatt
     4381 taattttctg attattctaa atatatacag aaagcgcttt cctaggattt tatatctaag
     4441 gaggaagtaa caatgaaaaa taa
//
