LOCUS       NZ_CP059746             2056 bp    DNA     circular CON 01-OCT-2023
DEFINITION  Enterococcus faecium strain A4694 plasmid pA4694_P7, complete
            sequence.
ACCESSION   NZ_CP059746
VERSION     NZ_CP059746.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675385
            Assembly: GCF_012933245.2
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  JOURNAL   Unpublished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                     :: A4694
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 91.24x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/01/2023 03:42:29
            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)                     :: 3,020
            CDSs (total)                      :: 2,928
            Genes (coding)                    :: 2,815
            CDSs (with protein)               :: 2,815
            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)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 38 of 113
            Pseudo Genes (incomplete)         :: 69 of 113
            Pseudo Genes (internal stop)      :: 30 of 113
            Pseudo Genes (multiple problems)  :: 20 of 113
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059746.1.
            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="A4694"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA4694_P7"
                     /geo_loc_name="India:Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(join(2000..2056,1..165))
                     /locus_tag="HI848_RS14915"
                     /old_locus_tag="H4J15_014915"
     CDS             complement(join(2000..2056,1..165))
                     /locus_tag="HI848_RS14915"
                     /old_locus_tag="H4J15_014915"
                     /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            782..937
                     /locus_tag="HI848_RS14920"
                     /old_locus_tag="H4J15_014920"
     CDS             782..937
                     /locus_tag="HI848_RS14920"
                     /old_locus_tag="H4J15_014920"
                     /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            1004..1606
                     /locus_tag="HI848_RS14925"
                     /old_locus_tag="H4J15_014925"
     CDS             1004..1606
                     /locus_tag="HI848_RS14925"
                     /old_locus_tag="H4J15_014925"
                     /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"
     gene            complement(1742..1999)
                     /locus_tag="HI848_RS14930"
                     /old_locus_tag="H4J15_014930"
     CDS             complement(1742..1999)
                     /locus_tag="HI848_RS14930"
                     /old_locus_tag="H4J15_014930"
                     /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"
     Typing          complement(1665..1840)
                     /name="MOBV"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.01e-87"
     Typing          1005..1534
                     /name="rep_cluster_2351"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 gaaaagatag tttcttctac cggcagagcg atattctttt ccttcagtca gatgttcttt
       61 cgctaagcgc aaaacgtaag cttggttgta atcaagttct tgtgcaagtt cgctggtcgt
      121 cataatttcg gccaaagtga atttttctga ttttatcact ctcatttatg ctccttccat
      181 ttaacgtccg tctatattac gtgagtacgt cggacttacg acataagctt ataatataag
      241 ttttctgtgt tgtggtcaat tttatattat cgaaatgact agtagaaaaa atcaatgctc
      301 taaaaagggt ctattttgcg ttttaagcga tttagcgtct atttcgttta gttatcggcg
      361 caatcgttaa aacacgtaag agaagcgaga atggagcctg taaggcgact ggtagcgaaa
      421 cggtcgtgtt agattgcaaa agccgatagc tgaacgaaat agtaagcgtg gcgcctgcat
      481 atatttcggt agaaggaggt cggggttcgg ggcggagccc tgaggtttgt tttttggttt
      541 tggtgtttat gaattgggcg gaggaggggg ggactacgac acccccctta ttggtcattg
      601 gtcattggtc gatagctgtt tagccttact ctcccaaggg tttcagcgtt tttttttgac
      661 aaaatcagta atgccaaggg tttaaggcct attattcgct aattagtatc taaactgttg
      721 caccttagtt acttttttgt tactatggtt tttaagaaaa agtcgttgga ggatacgaat
      781 tatgatcagt aatgaaaaaa agagagtcgt tgtaacgctt actaaggaag tggcagataa
      841 tcttgataaa attgcgaaac aaatgggtct tagtaagtct ggtcttatta caatttgggt
      901 taatgctaac ggaaaggaaa atgagcaaaa aaaatagcaa aagcattagt gttggcgcac
      961 tgcttttgct gttagactgt tgttcaatta aggtaattat agcatgacga gtagaaaaac
     1021 taaagatgaa cgcacaagga attggacgtt tgtagtctat cctgaatcgg ctcctgaaaa
     1081 ttggagggag tttttagatg agttacatgt tccttgggtt gagagtccac ttcatgataa
     1141 agatgtgaat cctgacggtg aattgaaaaa gcctcattgg catgttttga taatgtttag
     1201 cggtaaaaag acgtatgatc aaatacgtga gataactcaa aagcttcggt ctccaaaccc
     1261 gcaaaaatgt gctaatgcaa aaggtatggt gcgatatttt gctcatatgg ataatccaga
     1321 aaaatttcaa tatgctaaaa gtgatattat cgctcatggt ggtgcagaaa ttgctagtta
     1381 tttgtcagta acgagtgcag aacgatatga gttgattaga gagatgatgt cgtttgttga
     1441 ttctaagaat atcactgaaa tcaaagattt aattgactat gcaatgtcag aaagatttga
     1501 tgattggttt ccgcttcttt gtgataattc agcttatatt atcgggcaat atataaaatc
     1561 gaatcgtcat ggtggaagtg taaattcaaa aataaataaa ggataagagc tgttaatttc
     1621 agctcttttt ttgtgcgtga aagtcttagt cactatgacc aaaactacgg acgaaactat
     1681 gaccaaaagt aggtactata ttatgaccga aaataggtcc aaaatggatt tttttgtgat
     1741 atcaaaaaat ataaggttgt tttgtaagaa aaccagttgg cacagccgac ttagccacct
     1801 tcctgtagga aggtgctatc agttttccct tatgctcttt ttgttcttca gagtttaatt
     1861 ccagaatatt tgtgagaagt aggtcaaaga ggtcggtggt ttcttcgact tttccgccgg
     1921 tcaattcgat aaaatcattg gaatatgatt ctagcaattt ttctagttgt tcaacgttga
     1981 tagttgtttc tttaggcatt tactcacctt ctttggtggt tatgactttt tctagttttt
     2041 taagggcttc tgggct
//
