LOCUS       NZ_CP018826             4374 bp    DNA     circular CON 03-APR-2024
DEFINITION  Enterococcus faecium strain ISMMS_VRE_12 plasmid p4_ISMMS_VRE12,
            complete sequence.
ACCESSION   NZ_CP018826
VERSION     NZ_CP018826.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03988631
            Assembly: GCF_001953235.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Bashir,A., Attie,O., Sullivan,M., Sebra,R., Singh,K.V., Altman,D.,
            Pak,T., Dutta,J., Chacko,K., Webster,E., Lewis,M., Hamula,C., Delli
            Carpini,K.W., Murray,B.E., Kasarskis,A., van Bakel,H. and
            Huprikar,S.
  TITLE     Genomic confirmation of vancomycin-resistant Enterococcus
            transmission from deceased donor to liver transplant recipient
  JOURNAL   PLoS One 12 (3), e0170449 (2017)
   PUBMED   28301471
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Bashir,A., Attie,O., Sebra,R., Singh,K.V., Altman,D., Pak,T.,
            Sullivan,M., Chacko,K., Lewis,M., Dutta,J., Hamula,C., Delli
            Carpini,K.W., Murray,B.E., Kasarskis,A., van Bakel,H. and
            Huprikar,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-DEC-2016) Genetics and Genomic Sciences, Icahn School
            of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY
            10029, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP3 v. v2.2.0
            Genome Coverage                   :: 278.48; 196.4
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001953235.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 02:06:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,103
            CDSs (total)                      :: 3,011
            Genes (coding)                    :: 2,879
            CDSs (with protein)               :: 2,879
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 45 of 132
            Pseudo Genes (incomplete)         :: 76 of 132
            Pseudo Genes (internal stop)      :: 34 of 132
            Pseudo Genes (multiple problems)  :: 19 of 132
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP018826.1.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="ISMMS_VRE_12"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p4_ISMMS_VRE12"
                     /geo_loc_name="USA: New York City"
                     /lat_lon="40.7127 N 74.0059 W"
                     /collection_date="2011-05-05"
                     /collected_by="Shirish Huprikar"
                     /note="Vancomycin-resistant Enterococcus faecium from an
                     infection of the liver of the donor of a liver transplant"
     gene            join(3408..4374,1..2)
                     /locus_tag="AL026_RS00275"
                     /old_locus_tag="AL026_00275"
     CDS             join(3408..4374,1..2)
                     /locus_tag="AL026_RS00275"
                     /old_locus_tag="AL026_00275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            5..238
                     /locus_tag="AL026_RS00280"
                     /old_locus_tag="AL026_00280"
     CDS             5..238
                     /locus_tag="AL026_RS00280"
                     /old_locus_tag="AL026_00280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            231..650
                     /locus_tag="AL026_RS00285"
                     /old_locus_tag="AL026_00285"
     CDS             231..650
                     /locus_tag="AL026_RS00285"
                     /old_locus_tag="AL026_00285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            659..967
                     /locus_tag="AL026_RS00290"
                     /old_locus_tag="AL026_00290"
     CDS             659..967
                     /locus_tag="AL026_RS00290"
                     /old_locus_tag="AL026_00290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            971..1333
                     /locus_tag="AL026_RS00295"
                     /old_locus_tag="AL026_00295"
     CDS             971..1333
                     /locus_tag="AL026_RS00295"
                     /old_locus_tag="AL026_00295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            1555..2961
                     /locus_tag="AL026_RS00300"
                     /old_locus_tag="AL026_00300"
     CDS             1555..2961
                     /locus_tag="AL026_RS00300"
                     /old_locus_tag="AL026_00300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          3492..4366
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1556..2958
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aagaatggca gaaaaacaaa agcattttgg taagaaaaat tggttggtga atttaacagg
       61 tgataacgtt gtcgttgttt ttttggatag caaaaaaatg tccggtaagt tacttgatgt
      121 aacgcagtat gagttgattt tgaaaaataa taaaattgat tccccaatca ttatccctaa
      181 gcatgctgtt aaatatgttt atggggtagc tgaaagtaac ggagaagata atgactgatt
      241 tgccagaaaa aatgaccata aaaaaccttg ctgatgagtt gggtatatct aaaaatacag
      301 tgcgcaatca actggtcaat gcaggttatg accttgctcg gtataaagat aatggggtta
      361 tcatgttaga caaggaattg attggtgttg tgcggtcaat ttatcggtca aaaggtggtc
      421 aattgactgg tgatttaccg gtcaatgatg caggcaatga tttcccgtta gaaaaagaaa
      481 atgaattttt gcgtgaacaa ttagcggaaa aagataggca tatttctgaa ttaacggaaa
      541 tgattcgtga ccaacaaaaa ttgactttgc ttcagcaaca aaaaaacgat cagttgttac
      601 tagaaaatca agaattaaaa aatcgaaaat ggtggcaatt ctggaagtga ggtgtgacat
      661 ggataaaatt gatttgagag aagaaacagt cgatagaatt gaattgatgt atgaacggtt
      721 agctgattat ttgaatttgc cggatgaaga taattatagt gaaatgcttg aacgaatgat
      781 ggatgttctc aactcggtta tcaatgctga tctagcaaaa tcttcagttt tgactaatga
      841 atttgttcat aagcatttag cgcaaacaac tgatgaatca gaaaaagaat tttggttgaa
      901 attaatgagt catgttatgc agttaaacca aatttccgtt attaattcca aagaaaagga
      961 gatgtagttt atgggaatga ctttagcaga tattaaagcg caagaagaaa aattaaaaaa
     1021 agaacaagcg aaacttcgcc aacagaaaaa acgcttgatt gagaaagaaa atgctgcaat
     1081 gggcaaggct cttcgcaagc gttttgggtt tgaaactttt gctgattttg agcggtggct
     1141 atcgtcgatt tctgacgatc agcaacacga aaaatcagtg gataatgagt ggcttgctga
     1201 tgaaaaatca gcgccaagcg aacgagatta tcccgatgaa tctgacggct tattcggagt
     1261 gataccgaat aagaaaagtc agatgagtga gagtaaattt acgtcaatat ttaatgacgt
     1321 gaatttacga taagcgatta ttttgcgtga agcaaaataa agcgtaaaag gagttgagag
     1381 cgtgacacgc tttcggctcc ttttttcgtt gtcacttgtg acagcgaata ccctcggaga
     1441 gcatttggaa ttgtgacagc catgtcacaa ttaggaaaat gttactcttt gacaaagagt
     1501 aacagaaagg tttacaatct ttttattagc gacagcgcga aggagggttt taacttgggg
     1561 tttagtattt catttaaaaa aggaacgaag aatacaagta tttctcataa taatcgtgag
     1621 ttaactgatc gccagaaaac caatgattgg cataagcata ttgacttcac gaaatcggat
     1681 gaaaatattt atttagagca gacgaatcta gcagataaat atgaggaatt gtttggcgaa
     1741 gtggtagaaa aatataatgc gaaacaaaaa agagccgata gaaaaatcga ggactattta
     1801 gcgaaagtgc gcaaggataa aaagttggaa cctcaacgag aatttattgt gcaaataggc
     1861 attttagatg atttccagac aaatcgagca gatggttctt ctactggcat atcgaaacaa
     1921 caagctgaac aaaatcgagt gattgccaat aaaattttgg ttcagtatta caaggagttt
     1981 caagagagaa accctaattt ggctgtttat aatgctgtta ttcataatga cgaaataagt
     2041 ccgcacctgc acttgaatat tgtgccggtt gctgaaggtt ataaacgggg tgttcaaaag
     2101 cagccgagct ttaataaagc actggttcaa caagggatac acgctgataa agataatggt
     2161 cgagtgcttt tcaataattt tagaaatcaa gaagttgact ctatagaacg attaatgaat
     2221 gattacggtt ggaaaaggga tattgtcggt accaacaaaa ttaaagatat tcacgaatac
     2281 aaagaaatca tgagtgaaat ttctgaattg cgccaaacgg ctgtaaaaga gcgtgagagc
     2341 gtttctgatg agttgaggta tatttctagg caaagagaag aaaacgagcg tgataaggct
     2401 ctgatggctt ctgagagagc gaagattgaa gaagagaaga aaaatatgct gaatgtaaaa
     2461 aaagagatgg cggtcatttt ccaaaaagat atggttcctt tagaaagttt caagaggctt
     2521 cctgatggtt cgtatcattt atctgggaat gattttgttg atttgtatca acgagctacg
     2581 agagcaacaa atgccaagag aaatgctgat aacatgagtg agcaatattt acagatgctt
     2641 gagcaaaata cagaattaaa tgagtatgta gctacattgg aagaagagcg tcatttgtct
     2701 ggtagaaaac aattagcaga tttacaagtg gaaaataaaa agctgaaaga agaaaatcgc
     2761 tctttacgcc agcgtttaga gcgattaaaa aacgcatttc aaaaatcgat cactcgtttg
     2821 tctatccgtt ttggtcttgc agaaaaggat atggggcttt ctgaggaatt agaagtgtta
     2881 gagcaggaga aaaccttatt ttatcgtcaa aacgtctcac agcgtaaatt agagcgttct
     2941 gaagatgaga tcgagtggta gttacgatgt gcagtcaacg gtaccggagg cggtttgtgc
     3001 cgaggataag gagttgacgg ctaaaccact agcctattaa gctgacattt gctaaaaaat
     3061 ggccagtcca ttttttggcc aacctagcgt tagcgaagtt tgggggcgcc cttttcaaag
     3121 ggtgcggttt tattttttgg atatttgcat agctaaagag aagtgctatt attgagttag
     3181 caaacaaatg aactgaaaaa agagtaaaaa aatagtcgag caacgctacc aacgttctcg
     3241 acctttacgg aaactaatcg cactagctcc gtaacttctt aatcattata cgaatatttt
     3301 tagatttctt caagactaga gattttttgg taatgaattt ttaagagtta cgtgaacttt
     3361 tgaaaattct ttccagaagt ctctttttct ttgaggagga acaaaatttg agtaaaaatg
     3421 gcataatcgt aaatgagtgg gaaaatttaa cagccctatc taacaggcgg ttaaatgtac
     3481 aaaatatgta caccccctta aaaatgcagt ggtcaattga ccgaattact atcgttggaa
     3541 aactgaagga aaatatttat tatcacactc aaaatgatgt gttgatttta gattttgagc
     3601 aattaatgcg ggtgaatgaa ggcaatggct atttaaaagc ggttgggaat aacggctggc
     3661 aattattaga ccaatacgaa gaaaatattg cttatattga gattttgaaa tggcaagatg
     3721 gcaaagggcg gattgatttt aacccgaata agattggtca ttttttagct agttcaatga
     3781 aaaatttcat tcatgattta tttctagaac cacatttctc acgtgcggat attgcttgcg
     3841 atattatcga tgtgcctgat gagtttatta cacaatatcg agtggttgat cctgtttctt
     3901 tcaagccaat ttatgggcgg tctgggaagc tggaaacagc ttattggggc agtcgtgcca
     3961 gcgaacgcca gattcggcta tacaacaaaa aattggaaca ggaaaccaag cgtaaaattg
     4021 tgccaccaga aatagaaact tggtggcgac tggaattgca gttaaggcgt gggaaagcaa
     4081 cagattggca tgcaatggtt catgaaagtt taaatagttt tgctagccct cattttctac
     4141 cacttgatgt aaaaacaaat gataaggtga tgatttttgg actgattgct aaccctgaaa
     4201 tgtgggggtt tttagagcgt agaatgaaat acaaattgag agatattttg aaaagagaaa
     4261 gtcaaaatga tgagttgacg aatcatttac gagaaacatt ttcggaatca gcagatgttt
     4321 tgaaaaaaga attagacact tggcttcaag ggttagatgt aacggaggag gaat
//
