LOCUS       NZ_CP016167             2125 bp    DNA     circular CON 22-APR-2024
DEFINITION  Enterococcus faecium strain ISMMS_VRE_11 plasmid ISMMS_VRE11_p4,
            complete sequence.
ACCESSION   NZ_CP016167
VERSION     NZ_CP016167.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03988630
            Assembly: GCF_001721905.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2125)
  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 2125)
  AUTHORS   Bashir,A., Attie,O., Sebra,R., Singh,K.V., Altman,D., Pak,T.,
            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 (21-JUN-2016) Genetics and Genomic Sciences, Mount Sinai
            School of Medicine, 1425 Madison Avenue, New York, New York 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. May-2014
            Genome Coverage                   :: 38.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001721905.1-RS_2024_04_22
            Annotation Date                   :: 04/22/2024 02:03:03
            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)                     :: 3,111
            CDSs (total)                      :: 3,018
            Genes (coding)                    :: 2,815
            CDSs (with protein)               :: 2,815
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 132 of 203
            Pseudo Genes (incomplete)         :: 69 of 203
            Pseudo Genes (internal stop)      :: 30 of 203
            Pseudo Genes (multiple problems)  :: 24 of 203
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP016167.1.
            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..2125
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="ISMMS_VRE_11"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="ISMMS_VRE11_p4"
                     /geo_loc_name="USA: New York City"
                     /lat_lon="40.7127 N 74.0059 W"
                     /collection_date="2011-05-24"
                     /collected_by="Shirish Huprikar"
     gene            complement(468..638)
                     /locus_tag="AL025_RS16790"
     CDS             complement(468..638)
                     /locus_tag="AL025_RS16790"
                     /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_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            complement(654..1193)
                     /locus_tag="AL025_RS16185"
                     /old_locus_tag="AL025_15425"
     CDS             complement(654..1193)
                     /locus_tag="AL025_RS16185"
                     /old_locus_tag="AL025_15425"
                     /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_002289340.1"
                     /translation="MQPKETFTIKELSELFEISRQAISKHVDKLDPSLLAKNERGYKVV
                     LRSGVLQLASNLGNQRLLYRLHEYEQENDKNVYISSKNVIVNELLDKLREENEFLREQL
                     SLKEQNNSNMQKLLDQQQQLTLQANQQIEKLQEQLQLAYTEETPEDESTTILSEETESI
                     EKHTKKKKQKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            complement(1221..1958)
                     /locus_tag="AL025_RS16190"
                     /old_locus_tag="AL025_15430"
     CDS             complement(1221..1958)
                     /locus_tag="AL025_RS16190"
                     /old_locus_tag="AL025_15430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015060391.1"
                     /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_002305239.1"
                     /translation="MSNDIVRYNNGLNSVPLRKFTPIDMDLFWGICSKMKRKGTKEEIF
                     TFKQIKELIDYNINARGDRFANDLIKMSKKIITLSFIYEDEKTYEQLNLFQKFKIDKVN
                     ETLLIKVSEEFEYILNSIGTNFTRFELENMTNLKSSYVKELYRQLMAHKDRRSKKGHWF
                     VKIEDFRALLAIPESYRMRDIDKQIFAQAKKEFLNVNSTHPAIFKTFEIKKIKAYKGNK
                     IGSLQIYFEENIPSITLDNWLEK"
                     /name="replication initiation protein"
     Typing          complement(1222..1958)
                     /name="rep_cluster_1742"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttacacatg gaatatttac ttggtttgct ctatctggat taatagtaat agatatctta
       61 aattattttt atatttacta ttcttattta aaaaatgaaa aattttttta tacaatgttt
      121 ttccccctag ttattttgat tattttatta agctaatatg aagtagttag ttatttaatt
      181 gcatagttga cataatgtac actatgccaa gtagcccctc taccaatgga tagagacgct
      241 cactttgtga tttttaattg gtctagctaa aagcaacttt ctaaagcttg atttttcgcg
      301 gttatctata tctaattctt tgtgcatttt tatctgtcat ttttttaaga cttgttattt
      361 tttgtaaaat atggtaaatt tttggtagcg cttcataagc gcgtgctttt tcaagaataa
      421 acactcatta ttttttaact ggctgctcgg aagagcagtc ttttttatta tttatccgtc
      481 tcttttacaa acaattcttc gttaggactg ttgtaataat ttggattcaa tttcaattca
      541 ccatgtttat tccctttatt gattactgac aataacatcg gactgaagcc tagaattcct
      601 agtaaaatag aaccgaatag aagatttttt cttgtcatga atgttccctc cagttatttc
      661 caaagttgcc accatttttg cttcttcttt tttgtgtgtt tttctatcga ttctgtttct
      721 tcagaaagaa tagtagttga ttcatcttct ggagtttctt ccgtataagc taattgtaac
      781 tgttcttgca gtttttcgat ctgttgattt gcctgtaggg tgagctgttg ttgctggtcg
      841 agtaattttt gcatattaga attattttgc tctttgaggg aaagttgttc tcgtaaaaat
      901 tcattttctt cacgcaactt atctagcaac tcgtttacaa tcacgttttt gcttgatata
      961 taaacgtttt tatcgttttc ttgttcatac tcatgcaacc tatatagtaa cctttggtta
     1021 cctaagttgc tagcaagttg caatactcca gaacgtaata caaccttata accacgctca
     1081 tttttagcta ataaggacgg gtctaattta tcaacatgtt tagagattgc ttgcctactt
     1141 atttcaaata attcagataa ttcctttatt gtaaaggttt ctttgggttg catgataatt
     1201 gcctcctaaa ttgttaggta ttatttctct aaccaattat ctaaggtaat tgaaggtata
     1261 ttttcttcaa aataaatttg cagagatcct atcttatttc ctttgtaggc tttaattttt
     1321 ttgatttcaa aagttttaaa aatagcaggg tgagttgaat taacgtttaa aaattctttt
     1381 ttcgcttggg caaaaatttg tttatcaata tctctcatgc gataactttc tggtattgct
     1441 aatagagctc taaaatcttc tatttttaca aaccagtgac cttttttaga tcttctgtct
     1501 ttatgagcca taagttggcg atataactct ttaacgtagc tactctttaa gtttgtcata
     1561 ttttctaatt cgaaacgagt aaaattagtt ccgattgaat taagtatata ttcaaattct
     1621 tcagaaacct ttattaataa tgtttcattc actttatcga ttttaaattt ttgaaacaga
     1681 tttaattgtt catatgtttt ttcgtcttca taaataaaag acaaagtaat gatttttttt
     1741 gacattttta ttaaatcatt agcaaaacgg tcgccacgtg catttatatt gtaatcaatt
     1801 aattctttta tttgtttaaa tgtaaaaatt tcttcttttg taccttttct tttcatttta
     1861 gaacatattc cccaaaataa atccatatct ataggggtaa attttcttaa agggacagaa
     1921 tttaatccat tattatatcg aactatatcg ttactcaata aaaatcacct caataaatta
     1981 tgttatcata gacataagag gatgtaaaac acaatttatc cccccatagt gtgacaattt
     2041 atcccccata gtgtgacaat ttatccccca tagtgtgaca atttatcccc atagtgtgac
     2101 aatttatccc ccactaccta tgtca
//
