LOCUS       NZ_CP059822             2056 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain BP657 plasmid pBP657_P6, complete
            sequence.
ACCESSION   NZ_CP059822
VERSION     NZ_CP059822.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675395
            Assembly: GCF_012933075.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2056)
  AUTHORS   Veeraraghavan,B., Vasudevan,K., Arumugam,A., Solaimalai,D. and
            Bakthavatchalam,Y.D.
  TITLE     Complete genome of vancomycin resistant Enterococcus faecium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2056)
  AUTHORS   Veeraraghavan,B., Vasudevan,K., Arumugam,A., Solaimalai,D. and
            Bakthavatchalam,Y.D.
  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 2056)
  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                     :: BP657
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 44.03x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 06:25:27
            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)                     :: 3,092
            CDSs (total)                      :: 2,999
            Genes (coding)                    :: 2,883
            CDSs (with protein)               :: 2,883
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 38 of 116
            Pseudo Genes (incomplete)         :: 72 of 116
            Pseudo Genes (internal stop)      :: 30 of 116
            Pseudo Genes (multiple problems)  :: 20 of 116
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059822.1.
            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..2056
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BP657"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pBP657_P6"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2017"
                     /collected_by="CMC Vellore"
     gene            complement(join(1842..2056,1..43))
                     /locus_tag="HI829_RS15275"
                     /old_locus_tag="HI829_015275"
     CDS             complement(join(1842..2056,1..43))
                     /locus_tag="HI829_RS15275"
                     /old_locus_tag="HI829_015275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002377879.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002299941.1"
                     /translation="MPKETTINVEQLEKLLESYSNDFIELTGGKVEETTDLFDLLLTNI
                     LELNSEEQKEHKGKLIAPSYRKVAKSAVPTGFLTKQPYIF"
                     /name="hypothetical protein"
     gene            complement(44..265)
                     /locus_tag="HI829_RS15280"
                     /old_locus_tag="HI829_015280"
     CDS             complement(44..265)
                     /locus_tag="HI829_RS15280"
                     /old_locus_tag="HI829_015280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299940.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002299940.1"
                     /translation="MRVIKSEKFTLAEIMTTSELAQELDYNQAYVLRLAKEHLTEGKEY
                     RSAGRRNYLFSPEALKKLEKVITTKEGE"
                     /name="hypothetical protein"
     gene            882..1037
                     /locus_tag="HI829_RS15285"
                     /old_locus_tag="HI829_015285"
     CDS             882..1037
                     /locus_tag="HI829_RS15285"
                     /old_locus_tag="HI829_015285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299939.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CopG family transcriptional regulator"
                     /protein_id="WP_002299939.1"
                     /translation="MISNEKKRVVVTLTKEVADNLDKIAKQMGLSKSGLITIWVNANGK
                     ENEQKK"
                     /name="CopG family transcriptional regulator"
     gene            1104..1706
                     /locus_tag="HI829_RS15290"
                     /old_locus_tag="HI829_015290"
     CDS             1104..1706
                     /locus_tag="HI829_RS15290"
                     /old_locus_tag="HI829_015290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_002323513.1"
                     /translation="MTSRKTKDERTRNWTFVVYPESAPENWREFLDELHVPWVESPLHD
                     KDVNPDGELKKPHWHVLIMFSGKKTYDQIREITQKLRSPNPQKCANAKGMVRYFAHMDN
                     PEKFQYAKSDIIAHGGAEIASYLSVTSAERYELIREMMSFVDSKNITEIKDLIDYAMSE
                     RFDDWFPLLCDNSAYIIGQYIKSNRHGGSVNSKINKG"
                     /name="replication protein"
     Typing          complement(1765..1940)
                     /name="MOBV"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.01e-87"
     Typing          1105..1634
                     /name="rep_cluster_2351"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 atttttctag ttgttcaacg ttgatagttg tttctttagg catttactca ccttctttgg
       61 tggttatgac tttttctagt tttttaaggg cttctgggct gaaaagatag tttcttctac
      121 cggcagagcg atattctttt ccttcagtca gatgttcttt cgctaagcgc aaaacgtaag
      181 cttggttgta atcaagttct tgtgcaagtt cgctggtcgt cataatttcg gccaaagtga
      241 atttttctga ttttatcact ctcatttatg ctccttccat ttaacgtccg tctatattac
      301 gtgagtacgt cggacttacg acataagctt ataatataag ttttctgtgt tgtggtcaat
      361 tttatattat cgaaatgact agtagaaaaa atcaatgctc taaaaagggt ctattttgcg
      421 ttttaagcga tttagcgtct atttcgttta gttatcggcg caatcgttaa aacacgtaag
      481 agaagcgaga atggagcctg taaggcgact ggtagcgaaa cggtcgtgtt agattgcaaa
      541 agccgatagc tgaacgaaat agtaagcgtg gcgcctgcat atatttcggt agaaggaggt
      601 cggggttcgg ggcggagccc tgaggtttgt tttttggttt tggtgtttat gaattgggcg
      661 gaggaggggg ggactacgac acccccctta ttggtcattg gtcattggtc gatagctgtt
      721 tagccttact ctcccaaggg tttcagcgtt tttttttgac aaaatcagta atgccaaggg
      781 tttaaggcct attattcgct aattagtatc taaactgttg caccttagtt acttttttgt
      841 tactatggtt tttaagaaaa agtcgttgga ggatacgaat tatgatcagt aatgaaaaaa
      901 agagagtcgt tgtaacgctt actaaggaag tggcagataa tcttgataaa attgcgaaac
      961 aaatgggtct tagtaagtct ggtcttatta caatttgggt taatgctaac ggaaaggaaa
     1021 atgagcaaaa aaaatagcaa aagcattagt gttggcgcac tgcttttgct gttagactgt
     1081 tgttcaatta aggtaattat agcatgacga gtagaaaaac taaagatgaa cgcacaagga
     1141 attggacgtt tgtagtctat cctgaatcgg ctcctgaaaa ttggagggag tttttagatg
     1201 agttacatgt tccttgggtt gagagtccac ttcatgataa agatgtgaat cctgacggtg
     1261 aattgaaaaa gcctcattgg catgttttga taatgtttag cggtaaaaag acgtatgatc
     1321 aaatacgtga gataactcaa aagcttcggt ctccaaaccc gcaaaaatgt gctaatgcaa
     1381 aaggtatggt gcgatatttt gctcatatgg ataatccaga aaaatttcaa tatgctaaaa
     1441 gtgatattat cgctcatggt ggtgcagaaa ttgctagtta tttgtcagta acgagtgcag
     1501 aacgatatga gttgattaga gagatgatgt cgtttgttga ttctaagaat atcactgaaa
     1561 tcaaagattt aattgactat gcaatgtcag aaagatttga tgattggttt ccgcttcttt
     1621 gtgataattc agcttatatt atcgggcaat atataaaatc gaatcgtcat ggtggaagtg
     1681 taaattcaaa aataaataaa ggataagagc tgttaatttc agctcttttt ttgtgcgtga
     1741 aagtcttagt cactatgacc aaaactacgg acgaaactat gaccaaaagt aggtactata
     1801 ttatgaccga aaataggtcc aaaatggatt tttttgtgat atcaaaaaat ataaggttgt
     1861 tttgtaagaa aaccagttgg cacagccgac ttagccacct tcctgtagga aggtgctatc
     1921 agttttccct tatgctcttt ttgttcttca gagtttaatt ccagaatatt tgtgagaagt
     1981 aggtcaaaga ggtcggtggt ttcttcgact tttccgccgg tcaattcgat aaaatcattg
     2041 gaatatgatt ctagca
//
