LOCUS       NZ_CP059804             1935 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain BP3378 plasmid pBP3378_P11, complete
            sequence.
ACCESSION   NZ_CP059804
VERSION     NZ_CP059804.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675393
            Assembly: GCF_012933055.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1935)
  AUTHORS   Veeraraghavan,B.
  TITLE     Complete genome of vancomycin resistant Enterococcus faecium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1935)
  AUTHORS   Veeraraghavan,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2020) Clinical Microbiology, Christian Medical
            College, Ida Scudder Road, Vellore, Tamil Nadu 632004, India
REFERENCE   3  (bases 1 to 1935)
  AUTHORS   Veeraraghavan,B., Solaimalai,D., Vasudevan,K. and Arumugam,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-APR-2020) Department of Clinical Microbiology,
            Christian Medical College and Hospital, Ida Scudder Road, Vellore,
            Tamil Nadu 632004, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method :: CANU v. v. 1.7; UNICYCLER HYBRID v. v. 0.4.6
            Assembly Name                     :: BP3378
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 42.82x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 03:40:36
            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)                     :: 3,196
            CDSs (total)                      :: 3,103
            Genes (coding)                    :: 2,981
            CDSs (with protein)               :: 2,981
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 40 of 122
            Pseudo Genes (incomplete)         :: 74 of 122
            Pseudo Genes (internal stop)      :: 28 of 122
            Pseudo Genes (multiple problems)  :: 17 of 122
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059804.1.
            Bacteria and source DNA available from Christian Medical College.
            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..1935
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BP3378"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pBP3378_P11"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(<114..296)
                     /locus_tag="HI838_RS15845"
                     /old_locus_tag="HI838_015845"
                     /pseudo=""
     CDS             complement(<114..296)
                     /locus_tag="HI838_RS15845"
                     /old_locus_tag="HI838_015845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002313295.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-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"
     gene            complement(496..1461)
                     /locus_tag="HI838_RS15850"
                     /old_locus_tag="HI838_015850"
     CDS             complement(496..1461)
                     /locus_tag="HI838_RS15850"
                     /old_locus_tag="HI838_015850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305972.1"
                     /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_086322146.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(497..1378)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.969"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 aaatatgcca ttttagagct attgtagaaa atgtagtttg aaatgcaatt ttcttctttc
       61 agctttttat ttcccacttg taaatctgct aattattttc taccagacaa accattgatt
      121 ttttggctat cagttaactc acgattatta tgagaaatgc ttgtattctt tgttcccttt
      181 ttgaacgaaa tactaaaccc taaggtgaac ccctccttca cgctgtcgct aataaaaaga
      241 gtgtaaacct ttctgttact ctttgacaaa gagtaacatt ttcctaattg tgacatggct
      301 gtcacaattc caaatgctct ccgagggtat tcgctgtcac aagtgacaac gaaaaaagga
      361 gccgaaagcg tgtcacgctc tcaactcctt ttacgcttta ttttgcttca cgcaaaataa
      421 tcgcttatcg taaatccacg tcactaaaca ttgacgtaaa tttactctca ctcatctgac
      481 ttttcttatt cggtatcact tctctgtcac atccaacccc aaaagccacg tatccaattc
      541 tttttttaat tcgtctgcag attccttaaa agtctctcgt aaatgattcg tcaactcatc
      601 attttgactt tctcttttca aaatatctct caatttgtat ttcattctac gctctaaaaa
      661 cccccacatt tcagggttag caatcagtcc aaaaatcatc accttatcat ttgtttttac
      721 atcaagtggt agaaaatgag ggctagcaaa actatttaaa ctttcatgaa ccattgcatg
      781 ccaatctgtt gctttcccac gccttaactg caattccagt cgccaccaag tttctatttc
      841 tggtggcaca attttacgct tggtttcctg ttccaatttt ttgttgtata gccgaatctg
      901 gcgttcgctg gcacgactgc cccaataagc tgtttccagc ttcccagacc gcccataaat
      961 tggcttgaaa gaaacaggat caaccactcg atattgtgta ataaactcat caggcacatc
     1021 gataatatcg caagcaatat ccgcacgtga gaaatgtggt tctagaaata aatcatgaat
     1081 gaaatttttc attgaactag ctaaaaaatg accaatctta ttcgggttaa aatcaatccg
     1141 ccctttgcca tcttgccatt tcaaaatctc aatataagca atattttctt cgtattggtc
     1201 taataattgc cagccgttat tcccaaccgc ttttaaatag ccattgcctt cattcacccg
     1261 cattaattgc tcaaaatcta aaatcaacac atcattttga gtgtgataat aaatattttc
     1321 cttcagtttt ccaacgatag taattcggtc aattgaccac tgcattttta agggggtgta
     1381 catattttgt acatttaacc gcctgttaga tagggctgtt aaattttccc actcatttac
     1441 gattatgcca tttttactca aattttgttc ctcctcaaag aaaaagagac ttctggaaag
     1501 aattttcaaa agttcacgta actcttaaaa attcattacc aaaaaatctc tagtcttgaa
     1561 gaaatctaaa aatattcgta taatgattaa gaagttacgg agctagtgcg attagtttcc
     1621 gtaaatagtc gagagtgtta gcgcactgct cggcttttat tttgctcttt tttctcgttt
     1681 tctttgatta tagcactcct cctaaaaaaa taaaaagacc tcagggaatt tcattccccg
     1741 aaccccttga gcctcctcct gccgaaatgg aaagggcgca cccgctgttt atttcattca
     1801 gctatcggtt ttcacaatct aacacgatcg ttccgctacc agtcgcctta caggctccat
     1861 tttcgctcct ctaacgtgtt ttaacgattg tgccgataac taaacgaaat aaacgctaaa
     1921 accgctcaga acgca
//
