LOCUS       NZ_CP016169              832 bp    DNA     circular CON 22-APR-2024
DEFINITION  Enterococcus faecium strain ISMMS_VRE_11 plasmid ISMMS_VRE11_p6,
            complete sequence.
ACCESSION   NZ_CP016169
VERSION     NZ_CP016169.1
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 832)
  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 832)
  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
            CP016169.1.
            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..832
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="ISMMS_VRE_11"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="ISMMS_VRE11_p6"
                     /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            212..298
                     /locus_tag="AL025_RS16500"
     CDS             212..298
                     /locus_tag="AL025_RS16500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018113589.1"
                     /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_110300541.1"
                     /translation="MFELFICPLLVGVCVSLFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     gene            complement(418..>825)
                     /locus_tag="AL025_RS17255"
                     /old_locus_tag="AL025_15105"
                     /pseudo=""
     CDS             complement(418..>825)
                     /locus_tag="AL025_RS17255"
                     /old_locus_tag="AL025_15105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
ORIGIN
        1 tgtgagactc tgaaagcttg tctaagcgtt ctaagacaat tcttgattaa tttcccttaa
       61 tctagtcgag aagcgcctta caggcggtca ggcaagccct aacaacccta aaacaagtga
      121 tacttaaaaa caccacacaa atttaatttt ttaagatata aataacttgt cgcctatccg
      181 acagtcttgc gactggaagg aggtgtatct aatgtttgaa ctgttcattt gcccccttct
      241 tgtaggagtt tgtgtctctt tattcagtta ttggttgaat aaccgaaaca agaagtaaaa
      301 tcaataaagg cgacatcaac ctgaaaaaag ccccagagaa tccgacctct ctggggcttt
      361 cgtgtatcta atgtttgatc atttgcacat tcagtttaac atgattttaa atcaaattca
      421 attttgttgt tgctgatcta accattcctt gacacttttt agatagttta aggcggtttc
      481 tttttttgtc ggattttgca tgttagttgc ttgttgaagt aagatttcat agcgttcata
      541 tgtgacagat tgttgttttt cttttttttc ttcttcactg gcaaaccaag ggtttgttgt
      601 ctccaaatag atcactacag gcttcttcta tctttgtatc ttttacatat tgcacgtctt
      661 tttggttcgc tcatagttgt cttgaacctc tttttgctgt ttttctggca agttttgata
      721 aagacgagtg agtttttcca tgtttttatc cgtcaaacgt ttttcttgat tcacaaaaat
      781 atcgttcatt tcctcataac aagtggtaaa ctcttccatt tttttgtgct aa
//
