LOCUS       NZ_CP085912             6326 bp    DNA     circular CON 24-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762-D plasmid p6, complete sequence.
ACCESSION   NZ_CP085912
VERSION     NZ_CP085912.1
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 6326)
  AUTHORS   Zeng,W.
  TITLE     Acquisition of daptomycin resistance by Enterococcus faecium confers
            collateral sensitivity to glycopeptides
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6326)
  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
            CP085912.1.
            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..6326
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="SC1762-D"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p6"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            complement(4..954)
                     /locus_tag="LLE91_RS16315"
                     /old_locus_tag="LLE91_16315"
     CDS             complement(4..954)
                     /locus_tag="LLE91_RS16315"
                     /old_locus_tag="LLE91_16315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /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_065305730.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFVYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVIGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPTTTINEKIKQKKQELELLQQI
                     KQLEKEKEALEKQTESALSEKEKKNLLSDLDHLFR"
                     /name="replication initiation protein"
     gene            complement(1831..2520)
                     /locus_tag="LLE91_RS16320"
                     /old_locus_tag="LLE91_16320"
     CDS             complement(1831..2520)
                     /locus_tag="LLE91_RS16320"
                     /old_locus_tag="LLE91_16320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_065305728.1"
                     /translation="MAFYLPYLLIFVSISGSIWLSCKIYQTRHSLKGSKIRFKRFLLLG
                     CIFSLIIISSGLFGVLEGNKRISGSILLENVTQKYEVARDKKKKEQALTQKIEKFTACY
                     EDMSDIFVKQEKRLTDKNMETLTQLYRNLPEKQQKEYQEKYEQVKKDVQYVKDTQTEEA
                     CYDLFSDTIPFSTSEQERKERQQSVTYERYEILLQQATNMQNPTKKETALNYLKSVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            complement(2760..3698)
                     /locus_tag="LLE91_RS16325"
                     /old_locus_tag="LLE91_16325"
     CDS             complement(2760..3698)
                     /locus_tag="LLE91_RS16325"
                     /old_locus_tag="LLE91_16325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_065305727.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDHVQAHLLIQSFRPGEITAEKANQLGKEYAEKIAPEHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLDKCYDINDEICLTHGLSITERGKKEEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNPKTRTYDQFCDSLKIFGIHCFNRGKNFTYELIKKKKKVRS
                     NKLGKDYEKETILHELDRREQTYYRERERAYHRQQADELRRARESIRKIAGEVRREQRT
                     LTSEQPEIRPTQRNHEQHIERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3680..4060)
                     /locus_tag="LLE91_RS16330"
                     /old_locus_tag="LLE91_16330"
     CDS             complement(3680..4060)
                     /locus_tag="LLE91_RS16330"
                     /old_locus_tag="LLE91_16330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_002292464.1"
                     /translation="MSEQNQNLASDPSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(4382..4585)
                     /locus_tag="LLE91_RS16335"
                     /old_locus_tag="LLE91_16335"
     CDS             complement(4382..4585)
                     /locus_tag="LLE91_RS16335"
                     /old_locus_tag="LLE91_16335"
                     /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="WP_002321382.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            complement(4597..5130)
                     /locus_tag="LLE91_RS16340"
                     /old_locus_tag="LLE91_16340"
     CDS             complement(4597..5130)
                     /locus_tag="LLE91_RS16340"
                     /old_locus_tag="LLE91_16340"
                     /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="WP_002334266.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     gene            complement(5591..5761)
                     /locus_tag="LLE91_RS16345"
                     /old_locus_tag="LLE91_16345"
     CDS             complement(5591..5761)
                     /locus_tag="LLE91_RS16345"
                     /old_locus_tag="LLE91_16345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322958.1"
                     /translation="MTRKKLIFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            complement(5777..6310)
                     /locus_tag="LLE91_RS16350"
                     /old_locus_tag="LLE91_16350"
     CDS             complement(5777..6310)
                     /locus_tag="LLE91_RS16350"
                     /old_locus_tag="LLE91_16350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /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_104853326.1"
                     /translation="MQPQETFTIKELSELFKISRQALSKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQRLLDKLHEHEQNSDKNAYIPTKNVVANELLEQLREENKFLREQL
                     QEKDTQIKQMQKLLDQQQQLTLQANQQIDKLQKRLQLVYTEETSENESTTLSEETESIE
                     KQTKKKQKWWKLWK"
                     /name="DUF536 domain-containing protein"
     Typing          complement(5..953)
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.183"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2764..3698)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.705"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgctaccgg aataaatgat ctaaatcaga taataaattt tttttctctt tttccgaaag
       61 tgcagactct gtttgttttt caagagcttc tttctctttt tctagttgtt tgatttgttg
      121 gaggagttca agttcttgtt tcttctgttt gattttttcg ttaattgttg tagtaggctc
      181 ttcgtattct ttttgtttat cagctaaagc caatgcttta ttttgttctt ctttggttgg
      241 tgcatgtttg ttaaaatcgt ctgctttttt gatttctggt ttaaacgtaa attgatagcc
      301 aatgacaggt tttcctcgcc cttttccgta tttcttttta attgataatc ctttgaagat
      361 tgcggttaat tcctgacgta taggctttat aacacgatta tcaacgtttg cttggttgtt
      421 ccagtaactt tttggaatat ctaatagttc atgaaaatcc tctttagaaa aataaacaaa
      481 acctttagtt cgatattgtt ttagtaatcg aaacatagtt tttgcatagc tactttgtaa
      541 ttcgttaaat tgttggagtg aatagcgaac ccactcatct agattgttta gtaaaggtaa
      601 agctttttcg taaacttgta tatctacata tggatcttta gcagttccac gtattttaaa
      661 ctcactaaac ataacgaatc tatctatatc tagcccatta gcactccttt tgccaaaacg
      721 taaatccatt aatttatcat aagtcatttc taaatcattg atgaaacgat tattagcagt
      781 tgctttgtaa ttactcaaat cttttagctg gtcaaaagta agacgaacgg ttttatcgcc
      841 tttttcgcgc attctagaca caatagagaa aaatagattc atttcaactg gtgtaaattt
      901 ccgcaacgga atggtattta attcatgatg gtatttcacg atttcatttg ccaaatctat
      961 tcctccttac tctcccaaag gatacagacg ttataaacaa cgttttgtct gtgataatac
     1021 atattataac atacgtgagt ataaaaaaag agtttaaaag cagacaaaat gtagtttaaa
     1081 agcagacaaa atgtagttta aaagcagaca aaatgtagtt taaaagcaga caaaatgtag
     1141 tttaaaaaac gatgaatccc ttgagagagt aagaacataa ccgacagtaa agaaggttaa
     1201 aaagaggttt aaaaagagat ataaaaagag gggggcaaaa tttcccgcca aaaaaatcac
     1261 tatttttttc ctaaaacagg ttcgcgcatt tttttaaact gccaatcttg ctccctacgg
     1321 tcgctaaaaa ggtgtgatcg ctatgctctc acattgtact gcgcagtcgc ctaaaggctc
     1381 ctttgccaaa accgttcttc aaagagaacc ttgtggggct ctgatagctc gtctaaaccg
     1441 ttttgagaca gttctagggg aaaaccctta tctagttcct aaagcacctt acaggcggtc
     1501 agggcaagcc ctaacaaccc taaaataagg gatacttaaa aacaccacac agatttaatt
     1561 ttttaagata taataacttg tcgcctatcc gacagtcttg cgactggaag gaggtgtatc
     1621 ttatgattac ccactttatt tgcgcccttc ttgttgagct tctaaactct ttatttagtt
     1681 attggctgaa taaccgaaac aagaagtaaa atcaactaag gcgatatcag ctcacaaaaa
     1741 aagtcctaga gaatccgact tctctaggac tttcgtgtat cttatgatta cctatttgca
     1801 tatttagttt aacatgagtt tcaatcaaat tcaattttgc tgttgctgat ctaaccattc
     1861 cttgacactt tttagatagt ttaaggcggt ttcttttttt gtcggatttt gcatgttagt
     1921 tgcttgttga agcaagattt catagcgttc atatgtgact gattgttgtc gttcttttcg
     1981 ttcttgttcg ctagttgaaa aagggattgt atcactgaat aagtcataac acgcttcttc
     2041 cgtttgcgta tctttcacat attgcacgtc tttttttact tgttcatatt tttcttggta
     2101 ctctttttgc tgtttttctg gcaaattccg ataaagttga gtgagtgttt ccatattttt
     2161 atccgtcaaa cgcttttctt gcttcacaaa aatatcactc atgtcctcat aacaagcggt
     2221 aaatttttct attttttgcg ttaatgcttg ctcttttttc tttttatcac gtgctacttc
     2281 atacttttga gtgacatttt ctaataaaat acttcctgaa atgcgcttat tgccctctaa
     2341 aacgccgaat aagccgcttg aaatgattat taaggaaaat atacatccga gcaataaaaa
     2401 ccgcttaaat cgaattttag agcctttcaa tgaatgtctt gtttgataaa ttttacagct
     2461 gagccaaata cttcctgaaa tactaacaaa aatgagtaga tagggtaaat aaaatgccat
     2521 tttagcctcc ccatactaac caaaatgcga acagtgtcag gactaagcaa cataaggggg
     2581 caagaaaatc cattgatcgt tgaatgagcg cctttttttg ttctttattt cgctgatcta
     2641 atagctcttg atggagtttt ttaacttgta aatcaatcgt agtttgtatc ctttcttgtg
     2701 tgtagggagc aagaaaagca cgttgtttct ttatttcgtt ttctacgtct cgtaacgttt
     2761 tagagcgata attcttgttg gtggtctgtt cctctttcaa tgtgttgttc atgatttctt
     2821 tgagtcggtc taatttctgg ttgttcagac gtaagagttc gttgttctct tcgtacttct
     2881 ccagcaattt tccgaatgct ttctcgagct cttcgaagct cgtcggcttg ctgtctatga
     2941 taggctcgtt ctcgttctcg ataataggtt tgttctcgtc tgtccagctc atgtaaaatt
     3001 gtctcctttt catagtcctt tcctaatttg ttggatcgta cttttttctt ttttttgatt
     3061 aattcgtaag taaaattttt cccacgattg aagcaatgaa tcccaaatat tttgagggaa
     3121 tcacaaaatt ggtcataggt tctggttttt ggatttttca tggtttgatc aatggcaaag
     3181 cgaatctcgt ctttccaaac aggttcattt ttttctttta gtttgatttc agacatagtt
     3241 cgtttttctt ctttttttcc tcgttcagtg atacttaaac catgagtcaa acaaatttcg
     3301 tcgttgatat cgtaacactt atctaggaat gcttgaccat gtgcttgaaa cttttttcct
     3361 gtttctaaat tgaccgaatt aatgacaatg tgattgtgga tatggtcttt gtccgtgtgc
     3421 gtataaatcg cgatttggtg ttctggtgcg attttttcag cgtattcttt tcctagctgg
     3481 ttggcttttt cggcggtaat ttctcctggt cgaaaggact gaatcaataa gtgtgcttgt
     3541 acatgatcgt cttttccgta aagcatacgt atttgtttca tttcactttt ggcataatca
     3601 atgtcacagt ttattcctgt tttgacggtt gctcgtggtt ctgcgtaatt gattgctcgg
     3661 ctacaggaag tggttcgact tactttaact gttgccatat cttttgtagc tccttttgca
     3721 tgatttttag gttttcggat aagcgttggg cgtcgccagg agcaacgtcg tgttggtgtg
     3781 tattgcacca cttggcaatt tgattgatat tccctccagc tttggctaaa tcgcgcgcga
     3841 ttgcctgggc aatgtctggc gccactttcg gtgtcaccag acgcgcgttt tgtgccttgg
     3901 ctttcacgaa agccggcaca ctcatttgca aagcttcagc tgactgcttc agctttgcaa
     3961 attcggattc gctcactcga aaactgattt gttttggctc ggatcgatag gtatattttt
     4021 tagaaggatc gctagccaaa ttttgatttt gttcgctcat aagtcccacc ctttcagtac
     4081 gtcctacgga cgtatcgttc gcaatatcat tgtacctaaa aaggtacaat gagtaaagct
     4141 cactaaaagg gtttggcaag ctctatattt gctagccaaa tacctccgta tttggtgcaa
     4201 ataaccgctt gtcaaaggag cgcaagctcc cccttgaatc cccctcaaaa tccacgctcc
     4261 acaatacaaa aaaaggctag catttgctag ccactttttg taaagtttcg cttatttcac
     4321 cgaaggtgaa attgttgctt tgtaatattc aaacaaccct attcttctaa aatgtatcga
     4381 tttatttttt tttagacttt attatgtcta agacaactaa gattaacact aaaaataaac
     4441 cagatttgta taattgccct ccgcttagca tattaacaat tatagcaaca gctatagcaa
     4501 atataaaaat acgaatagta gctatttgcg gattcttttt agtaaatgtt tttaatgatt
     4561 ttaatgattt agatatcaaa aacatcactc cttaacttat aacgttgaat atctagtagc
     4621 tacaactctt ccagctgcat catatcccct ttggtaataa aatccaatcc agccattacc
     4681 atttttgtcc cattcttttg caactgcatt ccctggagaa gcaccttttt tagtccaact
     4741 tgcacctgtt aacaaagcac caattgccca acctgggata ccaaacatag aagtgctagc
     4801 tttccctcct gcccaaaagg cagcattaat agcattagca gctactccag tggttacagc
     4861 aatatttgta tattcctttt tgccccatct tgcaactgca gctcttgtca tgatatctga
     4921 agaatttgca aaatcttccg cactataacc atcctcatat ttagttacga ccataccatc
     4981 ttcagtgtac tcaataacta cattttcagt agcattgttt tcgtttaatg ataccacttg
     5041 ggaattttct gaagcataaa ctatagtagt tgacggtaaa acaactgccc caatagttaa
     5101 caaagctacc cctaaagtaa attttttcat agaatttcct cctgatacag aaaaatatat
     5161 agaaaacgtt ttctttgtga aaatcataaa acaaaaggta taggcttgtc aatattttat
     5221 ttagtaaaga taatttatat ttttgataat gtggtatagt tagaatgcat taggaaaata
     5281 tgttatatta aattcttgtt gacataatgt cgactatgcc aagtagcccc tctaccaatg
     5341 gatagagacg ctcactttgt gatttttaat tggtctagct aaaagcaact ttctaaagct
     5401 tgatttttcg cggttatcta tatctaattc tttgtgcatt tttatctgtc attttttaaa
     5461 gacttgttat ttttgagagg atttgatatg ctttttttat ctttcttata gttcttcatt
     5521 ttgtaatatt tttatgttga tgaataggat aatctcattt tgggctgctc gttagagcag
     5581 tcttttttta ttatttatcc gtttctttta caaataactc ttcgttagga ctgttgtaat
     5641 aatttggatt caatttcaat tcaccatgtt tatttccttt attgatcact gacaataaca
     5701 tcggactgaa gcctagaatt cctagtaaaa tagaaccaaa tatgagcttt tttcttgtca
     5761 tgaatgtttc ctccagttat ttccatagtt tccaccattt ttgcttcttc tttgtttgtt
     5821 tttctatcga ttctgtttct tcagaaagag tagttgattc attttctgaa gtttcttccg
     5881 tataaactaa ttgtaaccgt ttttgtagtt tgtcgatttg ttgatttgcc tgcaaggtga
     5941 gttgttgttg ctggtcgagt aacttttgca tttgttttat ttgagtatct ttttcttgga
     6001 gttgttcacg taaaaattta ttttcttcac gcaactgttc tagcaactca tttgcaacca
     6061 cgtttttggt tggtatataa gcatttttat cgctgttttg ttcatgttca tgcaacttat
     6121 ctagcaacct ttggttgcct aaattgcgag caagttgcaa tactccagaa cgcaatacaa
     6181 ccttataacc acgctcattt ttagctatca tggaagagtc taatttttgg atatgttttg
     6241 atagtgcttg cctacttatc ttaaaaagtt ctgacaattc ctttattgta aaggtttctt
     6301 gtggttgcat attggttgcc tcctgg
//
