LOCUS       NZ_CP085903             4463 bp    DNA     circular CON 23-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762 plasmid p9, complete sequence.
ACCESSION   NZ_CP085903
VERSION     NZ_CP085903.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22627481
            Assembly: GCF_020736585.1
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  JOURNAL   Unpublished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                   :: 200.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/23/2023 20:51:41
            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)                     :: 3,307
            CDSs (total)                      :: 3,216
            Genes (coding)                    :: 3,059
            CDSs (with protein)               :: 3,059
            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)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 63 of 157
            Pseudo Genes (incomplete)         :: 95 of 157
            Pseudo Genes (internal stop)      :: 38 of 157
            Pseudo Genes (multiple problems)  :: 30 of 157
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP085903.1.
            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"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p9"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            complement(314..748)
                     /gene="bacA"
                     /locus_tag="LK894_RS16430"
                     /old_locus_tag="LK894_16445"
     CDS             complement(314..748)
                     /gene="bacA"
                     /locus_tag="LK894_RS16430"
                     /old_locus_tag="LK894_16445"
                     /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            complement(1153..1326)
                     /locus_tag="LK894_RS16435"
                     /old_locus_tag="LK894_16450"
     CDS             complement(1153..1326)
                     /locus_tag="LK894_RS16435"
                     /old_locus_tag="LK894_16450"
                     /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"
     gene            complement(2007..2546)
                     /locus_tag="LK894_RS16440"
                     /old_locus_tag="LK894_16455"
     CDS             complement(2007..2546)
                     /locus_tag="LK894_RS16440"
                     /old_locus_tag="LK894_16455"
                     /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            complement(2562..3485)
                     /locus_tag="LK894_RS16445"
                     /old_locus_tag="LK894_16460"
     CDS             complement(2562..3485)
                     /locus_tag="LK894_RS16445"
                     /old_locus_tag="LK894_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"
     Typing          complement(2563..3485)
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttgtcaaag gggcgcaagc tcccccttga atccccctca aaacccacgc tccacaatac
       61 aaaaagtggc tagaaaatgc tagccacttt ttgtaaaatt tagtatgatt tatttttagc
      121 tatttagagt ttttatttcc gtaaatactt ctaaaaattg ctaagataaa tgctatagga
      181 attagataaa gaatactttt ttgtaagctt atattgaaaa ttagcctaaa tatgaagaac
      241 atagtgatta aaactattat tgaaataatt acagctaaaa tctttttatt catgagatag
      301 tttcactttc tgattatttt attacataac gagcgtaatc attgtattga tatgatgttg
      361 tattgctaaa gtgagcatta tatgttaatt gtacaccttt tccttgattt gcagctctta
      421 caaagacatt cattgcatca acagcactac taaaagcatt tgtaataacc catgttccaa
      481 ctccaccaat aggaataaaa gatgcaattt gagcaggagt ctttagctta ttataatttt
      541 ttttcaaatc tctacacatt ttattagtaa cataatagtt cattttatag caagtaaatc
      601 cacgatgatt atgattatat cgtgaacttg cagcttccac ttttatacct ctagcactaa
      661 aaggaaacag atttaacgga gtacttgctc caacaatcat accgaacaaa aatagacaag
      721 taataatttt aataatttta tttttcattg ttacttcctc cttagatata aaatcctagg
      781 aaagcgcttt ctgtatatat ttagaataat cagaaaatta aatattgtca agagggttta
      841 ttttataaaa cgtgttattt taaaggttag tagacataat gtcgagtatg ccaagtagcc
      901 cttgtatcaa ccgatacagg ggctcacttt gtgattttta attggtctag gtaaaaagct
      961 ctttttaagg cttgattttc tgcagttgct tctttccgtt tctttgtgaa tttttaccag
     1021 tcatttttta ctggattgtt atttttcata aaatatgata aatttttggt agcgctttat
     1081 aagcgcgttg ctttttcaag aataaacact cattattttt taactggctg ctcggaagag
     1141 cagtcttttt tattatttat ccgtttcttt tacaaacaat tcttcgttag gactgttgta
     1201 ataatttgaa ttcaatttaa gttctctgtt ggaattgttt tttccaatta cggataatag
     1261 catggggcta aaacctaata ttcctagaga aatagaaccc agtaccaaca cagttttttt
     1321 taacataggt tatacctcca ctttttttaa cgctaccact tgtatacaca ttttaaatac
     1381 tagccttcag tttatcaaat gtttaaattg aacggatata aatcaaaatt aaattttcaa
     1441 aagttgttct aaaaaatttt tcttttttgg aagttactct aacttttttt gcttgtggtg
     1501 cttggtatgt tttctccgcc tcccaggttc ttgaccattt tctctcaacg tggtaaaaat
     1561 cccacttata agagaaaatg gtcaagaacc tgggaggcgg agaatgccct taataccaag
     1621 caccgcaagc ctttcccata ctttattcga tgatcccacg atgatctcat aatgattcta
     1681 caatgaccct acgatgatca aaattctcaa aaaaaataaa cgaaatttca aacgattttt
     1741 ttgaaatttt gttaaaatca catttgtttt tttatgactt tttcaacaaa atcgattaga
     1801 atttattttg tttttccacc aaaaattgag tgagatttca acctatttta agcaataagt
     1861 caccatatag tttgatagtt tacaactata aacattgatt gtttacagtt gtaaactatt
     1921 ttttctttct cataaaaatt tgagtgatct ccccatcagg tagtacaact ttttcctcta
     1981 ctatccgaac taacttctag aaaattttag agattggttc tattagattt ccaaatttgc
     2041 caccactttt tttcaataag tggttgtgta ttgtctgctt ttttttcaga aaaggcagtt
     2101 gattcggttg ttggagtttc ttctgtataa gttaaatgga gctgttcttg taggttctca
     2161 atttgttggt tcgcttgtag agtgagttgt tgttgctggt cgagtaattt ttgcatttgt
     2221 tttatttgat tatctttttc ttgtagctgt atatcttttc gatttaactg tttttctagg
     2281 aaagaaagga gttttaattc ggaaacttgg ttggtgtttt tatggttttt ggtttttgat
     2341 ttttcgccaa ctagttttcg atttaagttt gcgttatcga ctaaaaacat tgattttata
     2401 gctttttgac cggtttcgtt aatcacaaac ttgtttccgt tttttgcaaa ccaaagtttt
     2461 cgatttttgt cagaaacttt tttgttaatt gctgttttac taactcctaa ttcttccgca
     2521 agttctttga ttgttttatc tgccataaat actccttaag cttaatcgaa taagttttgt
     2581 aaatttccta gtaaatcttg tttgagtttg tttgaaagtt ctcgtttttc tgcctgtttt
     2641 tcttcagttt gttgttgttg tttaaaatca gcttcatgag tgcctaaggg aagatttagt
     2701 attcgatctt tagcgcgcca tttttcttct cgtgttaatt ctccattgtg atcaatatta
     2761 aataatttta tacgtaaatc ttcttgtttc cctttggaaa aatcgtcagc atggttaatt
     2821 tcagctttcc aagtaaaacg ataaccgata acaggtttac ctcgaccttt accatatttt
     2881 ttacgaatag ttaatccttt aaataaggga gtgagttctt ctttaattgg ccttaagata
     2941 aatttgtcaa tatttgacgg actattccaa taacttttag gaatatctag taaatcaaaa
     3001 aatttttctt tggaaaattc agtccagcct tgagttcgat attgttttaa taatcgaaac
     3061 atagtttttg aatatgtgct atccaaatta gtaaattgct ctagattaaa tcttgtccag
     3121 ttctttaatt gattaaaaag tcctttaaat tctggattaa ctgaaattat aacaagttgt
     3181 ttatctcgta taatgctata ttttgtgaaa gcaacaaatt tagttaaagt atttccatca
     3241 tcattccaag cattaatact taataatttg tcatacgtgc tactaagatc ttttataaat
     3301 tgttccccac gttctgtata accgcttagt tttttcaaat cgtgaaatga aaaaataatc
     3361 tcatctacac ctttttcacg tacacgtgaa gcaattgaaa aaaataagtt catttcacga
     3421 ctattaaatt ttctcagagg aatatgattt aatctatttt catattttac aatttcattt
     3481 gccataagct tctcctactt ttataaagta tgaaataaaa gtaacatact ttataaaaat
     3541 actcaataat gtcggaaaac ctacttgaaa agcgtagaaa acctacttga aaagcgtaga
     3601 aaacctactt gaaaagcgta gaaaacctac ttgaaaaaac tctgaattgc ttgggagagt
     3661 aaggacacag ccgacataaa agagatataa aaagagatat aaaaagagat ataaaaagag
     3721 gggaggctaa ttttcccgcc taaaaaatca ctcctttttt ctctaaacag gttcgcgaat
     3781 ttatcaaaac tgccaattcc aaaccttgct ccctacggtt cgctaaaaag gtgtgatcgc
     3841 tctgctctca cattatactg cgcagtcgcc tccggctcct ttgctaaaag ccgttcataa
     3901 ggaacccttt gagaagctct gagcgttcgt ttaagacatt ttaagacagt cctagtataa
     3961 aaatccctta tcttgttctt aaaacgcctt acaggcggtc agggcaagcc ctaacaaccc
     4021 taaaattgtc taaatgccct ctaaaattcg atttaagcac tcttaaacct attcttatat
     4081 atttatatac ttaggcgttt caaacgtctt aaaacgcaaa ttagagcttg ataaagatat
     4141 ttgctcgtgt gcctagactt ttaaaaaagt cggcacacgc catgacaaag ctgaaataaa
     4201 ctgcttcagc tttgtcatgg cggattcgct cacttgaaaa agtgtttatt tcgctcgatt
     4261 attagcatat attttttagc ttttttgcta gccaaatttt gcattaattt gctcataagt
     4321 cccacccttt cagtacgtcc tacggacgta tcgttcgtaa tgtgaaagta cctttaaagg
     4381 tactttctac aaaactcact aaaagggttt ggcaagctct atatttgcta gccaaatacc
     4441 tccgtatttg gtgcaaataa ccg
//
