LOCUS       NZ_CP085901             6175 bp    DNA     circular CON 23-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762 plasmid p7, complete sequence.
ACCESSION   NZ_CP085901
VERSION     NZ_CP085901.1
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 6175)
  AUTHORS   Zeng,W.
  TITLE     Acquisition of daptomycin resistance by Enterococcus faecium confers
            collateral sensitivity to glycopeptides
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6175)
  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
            CP085901.1.
            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..6175
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="SC1762"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p7"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            1..945
                     /locus_tag="LK894_RS16330"
                     /old_locus_tag="LK894_16345"
     CDS             1..945
                     /locus_tag="LK894_RS16330"
                     /old_locus_tag="LK894_16345"
                     /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_002303559.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVEDLKATYEKILSLRFGRRSESGLSYDMFVMFTEFKINGD
                     VENPYVDIRIYEKALPLLNNLDEWVRYSLQQFNELQSGYAKTMFRLLKQYRTKGFAYFS
                     KEDFLELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQIKQ
                     LEKEKKALEKQTESALSEKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            966..1499
                     /locus_tag="LK894_RS16335"
                     /old_locus_tag="LK894_16350"
     CDS             966..1499
                     /locus_tag="LK894_RS16335"
                     /old_locus_tag="LK894_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_002363576.1"
                     /translation="MQPQETFTIKELSDLFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLDNQRLLDKLHKHEQNNDKNAYIPNKNVVANKLLDQLREENEFLREQL
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENSSTTLSEATETMD
                     EQTKNWKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1514..1684
                     /locus_tag="LK894_RS16340"
                     /old_locus_tag="LK894_16355"
     CDS             1514..1684
                     /locus_tag="LK894_RS16340"
                     /old_locus_tag="LK894_16355"
                     /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_032491833.1"
                     /translation="MTKKHLLFGSILLGILSFSPMLLSVANKGNKKGELKLNPNYYNSQ
                     NEEVFVEKLDK"
                     /name="hypothetical protein"
     gene            2139..2363
                     /locus_tag="LK894_RS16345"
                     /old_locus_tag="LK894_16360"
     CDS             2139..2363
                     /locus_tag="LK894_RS16345"
                     /old_locus_tag="LK894_16360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363584.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="class II bacteriocin"
                     /protein_id="WP_002363584.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="class II bacteriocin"
     gene            2383..2670
                     /locus_tag="LK894_RS16350"
                     /old_locus_tag="LK894_16365"
     CDS             2383..2670
                     /locus_tag="LK894_RS16350"
                     /old_locus_tag="LK894_16365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_002363589.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     gene            3121..3501
                     /locus_tag="LK894_RS16355"
                     /old_locus_tag="LK894_16370"
     CDS             3121..3501
                     /locus_tag="LK894_RS16355"
                     /old_locus_tag="LK894_16370"
                     /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_010782660.1"
                     /translation="MSEQNQYLASNHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVDPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3483..4397
                     /locus_tag="LK894_RS16360"
                     /old_locus_tag="LK894_16375"
     CDS             3483..4397
                     /locus_tag="LK894_RS16360"
                     /old_locus_tag="LK894_16375"
                     /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_010782659.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQIAIYTHTDKDHIHNHI
                     VINSVNLETGNKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYNQFCDSLKTFGIHCLNRGKNFTYELIHKKKKVRS
                     NKLGKDYEKETILHELDRRERAYNQQRTNELRRARASIRETAKEVRREQRTLTTEQPEI
                     RPTRRNHDQHVERGADYQQELSF"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4357..4635
                     /locus_tag="LK894_RS16365"
                     /old_locus_tag="LK894_16380"
     CDS             4357..4635
                     /locus_tag="LK894_RS16365"
                     /old_locus_tag="LK894_16380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002354385.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002369881.1"
                     /translation="MKEEQTTNKNYRSKTLQDIENEIKKQRAFLAPYTKERIQTTIDSQ
                     VKKFHHALLNQRNKEQKKVIMQRSMDILAPLCCLIMTLLAFWLVWGE"
                     /name="hypothetical protein"
     gene            4642..5332
                     /locus_tag="LK894_RS16655"
                     /pseudo=""
     CDS             4642..5332
                     /locus_tag="LK894_RS16655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     BGC             1..6175
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          2..945
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3484..4394
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggctaatg agattgtaaa ataccaccat gaattaaata caattccttt aagaaaattt
       61 acaccggttg aaatgaattt gtttttttcc atcgtgtcta gaatgcgtga aaaaggggat
      121 aagacagttc gttttacgtt tgaccaacta aaagatttaa gtaactacaa agcaactgca
      181 aatgtacgat ttgtagaaga tttaaaagca acttatgaaa aaatcttatc tttacgcttt
      241 ggtcgtagaa gtgagtctgg gctttcttac gatatgtttg taatgtttac agaatttaaa
      301 atcaacgggg acgtagaaaa tccttacgta gatatacgaa tttacgaaaa agcactgcct
      361 ttgttaaata atttagacga gtgggtacgc tattctttac aacaattcaa cgagctacaa
      421 agtggctatg caaagactat gtttcgtctg ttaaagcaat acagaaccaa aggtttcgca
      481 tatttctcca aagaagactt tcttgaatta ttagatattc ctaaaagtta taagcaacct
      541 gatatagata aacgagttat aaaacctata cgtcaagaac taactgcaat cttcaaagga
      601 ctaacaatca aaaagaaata cggaaaagga cggggaaaac ctgttattgg ctatcaattt
      661 acgttcaaac ctgagatcaa aaaagcagac gactttaaca aacatgcacc aaccaaagaa
      721 gaccaaaata aagcattggc tttagctgat aaacaaaaag aatacgaaga acccgctaca
      781 acaattaacg aaaaaatcaa acagaagaaa cgagaacttg aactcctcca acaaatcaaa
      841 caactagaaa aagagaaaaa agctcttgaa aaacaaacag agtccgcact ttcggaaaaa
      901 gagaaaaaaa gtttattatc tgatttagat aatttattcc agtagcaacc taggaggcaa
      961 ccagtatgca accacaagaa acctttacaa taaaggaatt gtcagatctt tttaagatga
     1021 gtaggcaagc aatatcgaaa catatccaaa aattagattc ttccatgata gctaaaaatg
     1081 agcgtggtta taaggttgta ttgcgttctg gagtattgca acttgctcgc aacttagaca
     1141 atcaaaggtt gctagataag ttgcataaac atgaacaaaa caacgataaa aatgcttata
     1201 taccaaacaa aaacgtggtt gcaaacaagt tgctagatca gttgcgtgaa gaaaatgaat
     1261 ttttacgaga acaacttgcc ctcaaagagc aaaataattc tcatatacaa aaactactcg
     1321 accagcaaca acaactcacc ctgcaagcca accaacaaat cgaaaaactt caggagcaac
     1381 tgcagttgac ttatacggaa gagtcttcag agaatagttc aacgactctt tctgaagcaa
     1441 cagaaacaat ggacgaacaa acaaagaatt ggaaaaaatg gtggcagcta tggaaatgaa
     1501 gaaggaaata cttatgacaa aaaaacactt gctattcggt tctatcctac taggaatatt
     1561 aagctttagc ccaatgttat tatcagtggc caacaaagga aataaaaaag gggaactaaa
     1621 actcaatcct aattactaca acagtcaaaa tgaggaagta tttgtagaaa aacttgataa
     1681 ataagaaaag actgctcgta cgagcagtct ttctgaaaga gattatccta ttattaacct
     1741 tagaaaagaa taataaatga atatgagata tgtaaaaagc ataacaaaca caaacaaaaa
     1801 taacaagtat ttaaaaaatg accgatcaat attcacaaag aattagaaag aaacaaccgc
     1861 agaaaaccaa gccttaaaaa gagcttttaa cctagaccaa taaaaattca caaaatcagc
     1921 gcctggatcc cttggtacag gcgttacttg gtagtatcga cattatgtct actagctgtt
     1981 taaataactg atcttataat tttatttaaa cgattatgaa ttcaaaacta ctttttatga
     2041 cgttaatcat tgttatataa taaaatgtta tataataaaa ttactaagat tatttaatat
     2101 aacaagcaat tttaaaaaaa cgaaaagaaa aaacaatcat gaaaaagaaa gtattaaaac
     2161 attgtgttat tctaggaata ttaggaactt gtctagctgg catcggtaca ggaataaaag
     2221 ttgatgcagc tacttactat ggaaatggtc tttattgtaa caaagaaaaa tgttgggtag
     2281 attggaatca agctaaagga gaaattggaa aaattattgt taatggttgg gttaatcatg
     2341 gtccatgggc acctagaagg tagtggtagg gaggttatta taatggattt tactaaagaa
     2401 gaaaaacttt taaatgcaat tagtaaagta tacaatgaag caactataga tgactatcct
     2461 gacttaaaag aaaagctctt tctttattct aaagaaatca gtgagggaaa aagtgttggt
     2521 gaagttagta tgaaattaag tagttttctt ggaagatata ttttaaaaca taaatttgga
     2581 ttacctaaat ctttaataga attacaagaa attgttagta aggaatctca agtatataga
     2641 ggatgggctt ctattggtat ttggagttaa ttctttggaa taaaatgaaa atgggactga
     2701 agaatcaatt ctgattcatc agtcccataa attatagagc cgaaaaatta tcatatttat
     2761 agatttatta atagtaaatg gcataagaat ctttgaacaa cgaaaaaaat gtagctctac
     2821 ctaattattg atttgcaaca atttcaccga aagtgaaaca agcgaaactt tacaaaaagt
     2881 ggctagcatt tgctagtctt ttttgtattg tggagagtgg ggggggaggg ggattcaagg
     2941 gggagcttgc gcccctttga caagcggtta tttgcaccaa atacgtaggt atttggctag
     3001 caaatataga gcttgccaag ccctttagta agctttagtg agctttactt attgtacctt
     3061 tttaggtaca atggtattgc gaacgatacg tccgtaggac gtactgaaag ggtgggactt
     3121 atgagcgaac aaaatcaata tttggctagc aatcattcta aaaaatatac ctatcgatcc
     3181 gagccaaaac aaatcagttt tcgagtgagc gaatccgaat ttgcaaagct gaagcagtca
     3241 gctgaagctt tgcaaatgag tgtgccggct ttcgtgaaag ccaaggcaca aaacgcgcgt
     3301 ctggtgacac cgaaagtggc gccagacatt gctcaggcaa tcgcgcgcga tttagccaaa
     3361 gctggcggga atatcaatca aattgccaag tggtgcaaca cacaccaaca cgacgttgat
     3421 cctggcgacg cccaacgctt atccgaaaac ctaaaaatca tgcaaaagga gctacaaaag
     3481 atatggcaac agttaaagta agccgaacca cttcttgtag ccgagcgatc aattacgccg
     3541 aaccacgagc aaccgtcaaa acagggataa actgtgacat tgattatgcc aaaagcgaaa
     3601 tgaaacaaat tcgcatgctg tatggaaaag acgatcgtgt acaagcacac ttattgatcc
     3661 agtcttttcg accaggagaa attaccgctg aaaaagccaa tcaactaggg gcagagtatg
     3721 cgaaaaaaat agcccctgac caccaaatcg cgatttacac acatacagac aaagaccata
     3781 ttcataacca cattgtcatt aactccgtca atctggaaac tgggaacaaa tttcaagccc
     3841 atggtcaagc atttttaaac aaatgttatg acctaaatga cgagatttgt cttgaacatg
     3901 acttaacaat cactgaacga gggaagaaac ccgaaaaacg aaccatgtct gaaatcaaat
     3961 taaaagaaaa aaatgaacct gtttggaaag acgaaattcg gtttgcgatt gatcaaacaa
     4021 tgaaaaacaa aaaaactcga acgtataacc aattttgtga ttctcttaaa acattcggca
     4081 ttcattgctt gaatcgtggg aaaaatttta cttacgaatt gatccacaaa aagaaaaaag
     4141 tacgatccaa caaactagga aaggattacg aaaaggagac gattttacat gagctggaca
     4201 gacgagaacg agcctacaat caacaacgaa ccaacgagct acgaagagct cgagctagca
     4261 ttcgcgaaac tgcaaaagaa gtacgaagag aacaacgaac tcttacgact gaacaaccgg
     4321 aaattagacc gactcgaaga aaccatgacc aacacgttga aagaggagca gactaccaac
     4381 aagaattatc gttctaaaac gttacaagac atagaaaatg aaataaagaa acaacgtgct
     4441 tttcttgcac cttataccaa agaaagaata caaactacaa ttgattcaca agtcaaaaaa
     4501 ttccaccatg cgctattaaa ccagcgaaat aaagaacaga aaaaagtaat tatgcagcga
     4561 tcaatggata ttcttgcccc cttatgttgc ttaatcatga cactgttagc cttttggctg
     4621 gtatggggag aataaataga aatggcattc tatttaccct atctactcat ttttgccagt
     4681 attttaggaa ttatttggct tagctataag gcttatcaaa caagatattc attaaaaggc
     4741 tctaaaattc gatttaagag gtttttattg ccaggggtta tattttacat tatcaatcgt
     4801 tttaagtggt ttattcggcg ttttagaggg aaataaacgt atttcaagaa gtattttatt
     4861 aggggatatc actcaaaagt atgaagcagc atgtgataaa aagaaaaagg agcaagtgtt
     4921 aacacaaaaa atggaagagt ttaccacttg ttatgaggaa atgaacgata tttttgtgaa
     4981 tcaagaaaaa cgtttgacgg ataaaaacat ggaaaaactc actcgtcttt atcaaaactt
     5041 gccagaaaaa cagcaaaaag aggttcaaga caactatgag cgaaccaaaa aagacgtgca
     5101 atattttaaa gatacgcaga cagaagaagc ttgttataat ttattcagtg atacaatccc
     5161 tttttcaact agtgaacagg aacgaaaaga acggcaacaa tcagttacct acgaacgtta
     5221 taaagcactg cttcagcaag caacgaacat acaaaatcca acgaaaaaag aaacggcatt
     5281 aaattatcta aaaagtgtca aggaatggtt agatcagcaa cagcaaaatt gaatttgatc
     5341 ggcaatcatg ttaaactaaa catgcaaatg atcaaacatt agatacacga aagccccaga
     5401 gaggtcggat tctctggggc tttttttcag gttgatgtcg cctttattga ttttacttct
     5461 tgtttcggtt attcaaccaa taactgaata aagagacaca aacttctata agaagggggc
     5521 aaatgaacaa ttcaaacatt agatacacct ccttccagtc gcaagactgt cggataggcg
     5581 acaagttatt atatcttaaa aaattaaact tgtgtggtgt ttttaagtat cgcttatttt
     5641 agggttgtta gggcttgccc tgaccgcctg taaggcgctt taaagctaga taaggatttt
     5701 tatccaagac tgtcttaaaa cggcttagat aagcattcag aaccgctcaa aggcctcttt
     5761 accaacatgt ttttagcaaa ggagccttta ggcgactgcg cagtacaatg tgagagcgta
     5821 gcgatcacac ctttttggcg accgtaggaa gcaaggtttt ggattggcag ttttgaaaaa
     5881 tgcgcgaacc tgtttaaaga aaaaagaagt ggtttttagg cgggaaaatt agcccccctc
     5941 tttttatatc tctttttaaa cctcttttta aacctcttta ccgtaagctg tgtccttact
     6001 ctaccaatgg atacagaatg ttatgaagga cattttgtct gtttatgaat gacattttgt
     6061 ctgtttatga atgacatttt gtctgtttat gaaggacatt ttgtctgttt gaacgtcaaa
     6121 tatgaatgtc ttgacattta aaaaatgtca ttcataattg gattgaggtg attat
//
