LOCUS       NZ_CP085914             5275 bp    DNA     circular CON 24-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762-D plasmid p8, complete sequence.
ACCESSION   NZ_CP085914
VERSION     NZ_CP085914.1
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 5275)
  AUTHORS   Zeng,W.
  TITLE     Acquisition of daptomycin resistance by Enterococcus faecium confers
            collateral sensitivity to glycopeptides
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5275)
  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
            CP085914.1.
            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..5275
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="SC1762-D"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p8"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            complement(join(4982..5275,1..693))
                     /locus_tag="LLE91_RS16410"
                     /old_locus_tag="LLE91_16410"
     CDS             complement(join(4982..5275,1..693))
                     /locus_tag="LLE91_RS16410"
                     /old_locus_tag="LLE91_16410"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_002322919.1"
                     /translation="MGATLALKGGKRGASALIGYVNRHGKLDRDRIYTHKLSAENKLAQ
                     TQLEATRRIFAKTGGIQAFHWVQSFDNSFDKNNPADVQKAHEIGAKLVDEIAKSYPNHE
                     IYMGTHTDSESGYIHNHIVFASIDTETGKKFHSDTEVGYHLQDLNDKVLLSFGIEQPKE
                     KFKQVDFEMHAEGKMSNREKMKHMILGAQDMSTDFDSFKKNLQEAYAVEVYEYNKGKRI
                     GFKWVDDEGKDFTIGGRKLGSDFERPAIERTLEFSQQKQEKEVEKPLETKPKVTNDDFS
                     ISGLKNLANDIRQQEERKKKEELQRQKEIERQQRSRPFYHDRGGMER"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(678..1034)
                     /locus_tag="LLE91_RS16415"
                     /old_locus_tag="LLE91_16415"
     CDS             complement(678..1034)
                     /locus_tag="LLE91_RS16415"
                     /old_locus_tag="LLE91_16415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323247.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_029404142.1"
                     /translation="MSEQKLNAENRKDSRQIKFRVSEDEYQYLTAIADQTGMSVPQLCK
                     SVALGMKYRAPNVDREGAIQIAKELRKYGGNLNQMARFINMNKGQMPSSSDLALMNQQL
                     SQIEKGVIDLWEQL"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            complement(1590..1955)
                     /locus_tag="LLE91_RS16420"
                     /old_locus_tag="LLE91_16420"
     CDS             complement(1590..1955)
                     /locus_tag="LLE91_RS16420"
                     /old_locus_tag="LLE91_16420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322917.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322917.1"
                     /translation="MAKMDIEDLEKKLAEARHDLSVKIGTNMVEKQGFKSYSAYNTFMR
                     NASKALKSSAGSAPAPAAAKPVATSAEKLPSELKAEAVQFQKQLEKWMEDNWGNKLDYK
                     TFYPELLEFFQKLNSLE"
                     /name="hypothetical protein"
     gene            complement(1964..2125)
                     /locus_tag="LLE91_RS16425"
                     /old_locus_tag="LLE91_16425"
     CDS             complement(1964..2125)
                     /locus_tag="LLE91_RS16425"
                     /old_locus_tag="LLE91_16425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322916.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322916.1"
                     /translation="MTAKTVTIDVEQLEKLLERHSDAIIEYTGGLSEETINQFDLLLTE
                     IIELDSKE"
                     /name="hypothetical protein"
     gene            complement(2115..2264)
                     /locus_tag="LLE91_RS16430"
                     /old_locus_tag="LLE91_16430"
     CDS             complement(2115..2264)
                     /locus_tag="LLE91_RS16430"
                     /old_locus_tag="LLE91_16430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322915.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322915.1"
                     /translation="MKKRLRKKMAKKNSSLDQAMKELMNYAKGERDGFLIHSYDEKGEQ
                     KNDG"
                     /name="hypothetical protein"
     gene            complement(2278..3027)
                     /locus_tag="LLE91_RS16435"
                     /old_locus_tag="LLE91_16435"
     CDS             complement(2278..3027)
                     /locus_tag="LLE91_RS16435"
                     /old_locus_tag="LLE91_16435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322914.1"
                     /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_002322914.1"
                     /translation="MGQPNKKADIALKDLLSRQDYLVVQGNDLAKAFGGLKSFEQRVLD
                     YCFSFVTKDSKLDDEYEVTALEIIKHFGLNTSGDSYRRIAEAFKKLNENTALYLRVERP
                     DGTQGLRMTQLFSWIDFYADGLVRFKFSADSAPYVLDLKEKFYSFRLGELSRINGKYAL
                     IMLKLWESYRRGKEKHTTITGDLEEWESWFLGKDKRLPAGQFFQKVITRAIEELSDKMS
                     VSFFVTTLKRGRKVVGYEITINDTSKE"
                     /name="replication initiation protein"
     gene            3742..3840
                     /locus_tag="LLE91_RS16440"
                     /old_locus_tag="LLE91_16440"
     CDS             3742..3840
                     /locus_tag="LLE91_RS16440"
                     /old_locus_tag="LLE91_16440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019775148.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="WP_110958386.1"
                     /translation="MYEKFLTLVVAPLFVGLVIELVSHWLDEKDDN"
                     /name="type I toxin-antitoxin system Fst family toxin"
     gene            complement(3994..4491)
                     /locus_tag="LLE91_RS16445"
                     /old_locus_tag="LLE91_16445"
     CDS             complement(3994..4491)
                     /locus_tag="LLE91_RS16445"
                     /old_locus_tag="LLE91_16445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322921.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322921.1"
                     /translation="MKLFFEKMGWHILPVVIILVGSYSLFCIFRSILEKFEEPKLKRVV
                     FALCFAFLALFVSVGISSYRPDVALSVRPKISKIEQLEAKAEAKQKKIDKISDQLEQAL
                     KIASQEKLKTFNPKDYPSEVITADWVQKNRDVIATLPDKELKDRYTKRFDDVESYFELN
                     SQ"
                     /name="hypothetical protein"
     gene            complement(4519..4974)
                     /locus_tag="LLE91_RS16450"
                     /old_locus_tag="LLE91_16450"
     CDS             complement(4519..4974)
                     /locus_tag="LLE91_RS16450"
                     /old_locus_tag="LLE91_16450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322920.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322920.1"
                     /translation="MPLDDFASKQELQKVKQELAEIKQQNQEVIETLKSLDNSVKQGYI
                     KVRGGEDIPKMSELKAEMNRYATYVQKRTAEIDQKLDSYGNISKSVSDELSRQVRPQVQ
                     KFLANDDRATAEELKQNRIANLMSVLASVGLFIGGTAILIVSVLKLL"
                     /name="hypothetical protein"
ORIGIN
        1 gccctcatca tcgacccatt tgaagccaat ccttttgcct ttattgtact cataaacctc
       61 gacagcatag gcttcttgaa gatttttttt gaaagaatca aaatcggtac tcatatcttg
      121 tgcgcccagg atcatatgct tcattttttc tcgattactc attttgccct cggcgtgcat
      181 ttcaaaatca acttgtttga atttttcttt cggctgttca atgccaaaac tcaataaaac
      241 cttatcgttt aggtcttgta ggtggtagcc gacctcggta tcagagtgaa attttttacc
      301 ggtttcagtg tcgatactgg cgaaaacaat gtgattatga atatagccgg attctgaatc
      361 ggtatgagtg cccatgtaga tttcatgatt gggatagctt tttgcgattt catcaacgag
      421 tttagcaccg atctcatgcg ctttttgcac gtccgccgga ttgtttttgt caaacgaatt
      481 atcaaacgat tgaacccaat gaaaggcttg aataccgcct gttttggcga aaatccgtct
      541 agtcgcttct agctgagttt gagccaattt attctcagct gacagtttgt gcgtataaat
      601 gcggtcacga tcaagctttc catgccgatt tacatagcca atcagcgcag aagccccacg
      661 tttaccgcct tttaaagcta aagttgctcc cataagtcaa tcaccccctt ttcgatttgc
      721 gaaagttgct ggttcatcaa ggctaaatct gaacttgaag gcatttgccc cttattcatg
      781 ttaataaagc gagccatctg attgagattt ccgccatatt tgcgcaactc tttggcaatt
      841 tgtatcgccc cctcccgatc aacgttcggc gctcgatact tcatgccaag tgccacgctc
      901 ttgcagagct gtggcacact cataccagtt tgatccgcaa tggcggtcaa atactggtac
      961 tcgtcttcgc tcactcgaaa tttaatttgc cgactatctt ttcgattttc ggcattcaat
     1021 ttctgctcgc tcatctcatc actcctcaaa taaaaatgct ccctattcgg tcgctttttt
     1081 cttctcgtca ttcttcgtgg tcgatattca aagctacaaa aacgctccct attcagtcgc
     1141 cttttttccg caatgaaatc tccctcggtt atgccactac aaaatgaaag ttccctactc
     1201 ggtcacttcc ctttttccgc tctataaccg aatgatttat taacctcatc atactcccta
     1261 ttcggtcgca taacaaggtt aataaatcat ataatacgca agcaccgcat ttggtaccca
     1321 aatacatcgc ttgtcgaggt ggcgttgccc cctacgaact cccccaatca cgcaacaaaa
     1381 agtagcctgt tcggctattt ttattacgtg atttcgcctc agaaaaagta gtctgttcga
     1441 ctatttttct actggctcat gcggtcaaac ttgcacgcaa gttgacctta tttttttgtt
     1501 tgcctgcgaa cagcgggcaa acaaaaaagc aagccaaaaa tcggcttgct cgttcttcaa
     1561 aaattgatcg catggactag ctcgttccgc tattccaagc tgttcaattt ttggaagaac
     1621 tctagcaact caggataaaa tgttttgtaa tccaacttgt ttccccagtt gtcttccatc
     1681 catttttcga gttgcttttg aaattgcacc gcttcggctt tcagctcgct aggcaatttt
     1741 tcggcagaag tggccaccgg ctttgcagct gctggcgcag gtgcagatcc ggcggacgac
     1801 ttcaatgcct ttgacgcatt ccgcatgaaa gtattgtagg cggaatagct cttgaaccct
     1861 tgtttttcaa ccatatttgt accgattttg actgaaagat catgccgagc ttcagctaat
     1921 tttttttcca aatcttcgat atccattttt gccatgcgta aactcactcc ttagaatcta
     1981 gttcgataat ttccgttaga agaagatcaa attggttgat cgtttcttct gaaagtccac
     2041 cggtgtattc aataatagcg tcactatgcc tttctaacag cttttcaagc tgttcaacgt
     2101 caatcgtaac tgtcttagcc gtcatttttt tgttctcctt tttcgtcata actatgaatc
     2161 aaaaagccgt cacgttcgcc ttttgcatag ttcattagtt ctttcatagc ttgatctagc
     2221 gaagaatttt tctttgccat ctttttacgc agtctttttt tcaactaaat cactcctcta
     2281 ttctttgctg gtgtcattga tcgtgatttc atatccaacg acttttcgcc cacgctttaa
     2341 ggttgtgacg aaaaatgaaa ctgacatctt atcagataat tcttcaatag cacgagtaat
     2401 tactttttga aaaaattgac ctgcaggaag gcgtttgtct ttaccaagaa accaagattc
     2461 ccattcttcc aaatcacctg taatcgttgt gtgtttttct tttcctctac ggtaggattc
     2521 ccagagtttt aacattatga gagcatattt cccattgatc cgagataatt cacctaaacg
     2581 aaagctataa aacttttctt tgagatcaag aacgtatgga gctgaatcag cagaaaattt
     2641 gaatcttact aacccgtcag cataaaaatc aatccaagaa aataattgcg tcattctgag
     2701 accttgagta ccatcggggc gctcgacacg aagataaagc gcagtatttt cattaagctt
     2761 tttgaaagct tcagctattc gacggtaaga atctccagag gtgttcaacc caaaatgttt
     2821 gataatttct aatgcggtta cctcgtattc gtcatctagt tttgaatctt tagttacaaa
     2881 gctaaaacag tagtctaaaa ctcgttgctc aaacgattta agccctccaa atgccttagc
     2941 taagtcgttt ccttgcacta ctaaataatc ttgacggctt agtaagtctt ttaatgcaat
     3001 atcagctttt ttatttggtt gtcccaaact gaaaatcctc cttttgtact ttttttaaaa
     3061 taataccatt tattcagttt ttttgcaata tttgaatttt caacgtggaa aatagtattt
     3121 ttgacgtgga aaatagtatt tttgacgtgg aaaatagtat tttcaacgtg gaaaatagta
     3181 tttataggcg ctacaaacgc tggtataaag ccattccttt tcccctaaag tattttaaag
     3241 tatttaaaag taatctataa agtattctct ttaagcgcgc gggtgagaaa aaaatttaaa
     3301 ttcaaaaaaa aaaaaatccc gcccaaacca gttgtctatt tttttccaac aggttcgcgc
     3361 atgaaataaa ctgcttctca catcatcgac aatttatccc ctttacctcg ttcaatctta
     3421 cagccacaag gcataaagga gtgatcgcta cgctctcaca ttttgcttac agcagtcgcc
     3481 tgcgctcctt cgttaaggtc aaaaccgttg ttcaaggagc ggttgggata ggcgtaaaag
     3541 cttgttgtag caagttttta gactgattta gattaaatcg ttagtcttgt tatacagcgc
     3601 ctttacaggc ggtcagggca agccctaacg acccaaaagc cccatctggt agaccatctt
     3661 ttttttgcag ggagtgaatg ctatattaat cttggcacta aagccaacta acgcttacac
     3721 aggttgggag gtgtattccg tatgtacgaa aaatttctaa cgttggttgt cgcaccgcta
     3781 tttgtcgggc tagtcattga gctagtttct cattggttgg acgagaaaga cgacaactaa
     3841 ggcttagtgc cttccaactc acacgcctag tcgcagggcg aaaaaaaagc cagacaccgt
     3901 cgcatggtgt ctggcttttg tgcattccgc actcgaaaaa attctaacgt tttcgcatgg
     3961 ttattatagc atggacgttg gcaaatctca atttcactga ctattcagct caaaatagga
     4021 ttctacatcg tcaaatcgct ttgtgtagcg gtctttcagc tctttatcgg gcaaagtagc
     4081 gatcacgtca cgattttttt gtacccaatc cgccgtaata acttcgcttg gatagtcttt
     4141 tgggttaaag gttttcagct tttcttgact ggcaattttc aatgcctgct ccagttggtc
     4201 cgaaatttta tcaatttttt tctgttttgc ttcggctttc gcttctagtt gctctatttt
     4261 gctgatttta gggcgtacag acagcgcaac gtccggacgg tatgaagaaa tgccgaccga
     4321 cacaaaaagc gctagaaacg caaaacagag ggcaaaaacg acacgtttca gctttggttc
     4381 ctcaaatttt tctaagatcg agcgaaaaat gcagaataaa ctatacgaac cgaccaaaat
     4441 aatcacgaca ggaagaatat gccaccccat tttttcaaag aacagtttca tttgcgtttt
     4501 aagccccctc tcgttcgatt acaggagctt taggactgaa acaataagaa tagcagtgcc
     4561 accgataaaa agccccacag aggctaatac ggacattaaa ttcgctattc gattttgttt
     4621 cagctcttcg gcagtcgctc gatcatcgtt ggctaaaaat ttttggactt gtgggcgcac
     4681 ttgccggctc aattcgtcag atacagattt gctgatatta ccgtagctat caagcttttg
     4741 gtcgatttca gcggttcttt tttgaacgta ggtggcgtag cggttcattt cagctttcag
     4801 ctcgctcatt ttgggaatat cttcgccacc tcgcaccttg atatagcctt gttttacgct
     4861 gttatcaagg cttttcagcg tttcaatgac ttcttgattt tgttgcttga tttccgctag
     4921 ttcctgcttc actttttgaa gctcctgctt acttgcaaaa tcatctaacg gcatatcgtc
     4981 actacctttc catgccacca cgatcatgat agaacgggcg agaacgttgt tgacgctcga
     5041 tttctttttg tcgttgcagc tcctcttttt tcttgcgttc ttcttgctga cgaatatcat
     5101 tagcaagatt tttcaaaccg ctgatagaaa agtcatcatt ggtgacttta ggcttggttt
     5161 caagcggttt ttcgacttct ttttcttgtt tttgttgaga aaattcaagt gttcgttcga
     5221 tcgcagggcg ctcaaaatca gaacctaatt ttcgtccgcc gattgtgaaa tcttt
//
