LOCUS       NZ_CP059782             1979 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Enterococcus faecium strain A3895 plasmid pA3895_P10, complete
            sequence.
ACCESSION   NZ_CP059782
VERSION     NZ_CP059782.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675384
            Assembly: GCF_012933265.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  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  JOURNAL   Unpublished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 1979)
  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 1979)
  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                     :: A3895
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 40.42x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/06/2023 04:47:14
            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)                     :: 3,060
            CDSs (total)                      :: 2,970
            Genes (coding)                    :: 2,868
            CDSs (with protein)               :: 2,868
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 35 of 102
            Pseudo Genes (incomplete)         :: 68 of 102
            Pseudo Genes (internal stop)      :: 25 of 102
            Pseudo Genes (multiple problems)  :: 20 of 102
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059782.1.
            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..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A3895"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA3895_P10"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(<255..437)
                     /locus_tag="HI845_RS15160"
                     /old_locus_tag="H4J14_015155"
                     /pseudo=""
     CDS             complement(<255..437)
                     /locus_tag="HI845_RS15160"
                     /old_locus_tag="H4J14_015155"
                     /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(637..1653)
                     /locus_tag="HI845_RS15165"
                     /old_locus_tag="H4J14_015160"
     CDS             complement(637..1653)
                     /locus_tag="HI845_RS15165"
                     /old_locus_tag="H4J14_015160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002326787.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVDDKV
                     HPLKLSWSIDRITIVGKLNDTIAYWTQNGVVFVDFEQLMRLNENQGYLKSVGTNGWQLF
                     DQYGEDIAYIEMLKFHPDKGRIDFNPNKIGEFLKGSMKQFIHDLFLDAHFSRADIACDI
                     LGVPDDFITQYRIVDPVSFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKQIV
                     PKEIETWWRIEMQLRRGKATDWHAMVRESLDSFASPHYLPGDVKPVDRIMIKGLNQDHS
                     EWAYISRNLKYRLRKLLKEESQNDELTNHLRETFKESANDLKIELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(638..1404)
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cattcagcta tcggttttca caatctaaca cgatcgttcc gctaccagtc gccttacagg
       61 ctccattttc gctcctctaa cgtgttttaa cgattgtgcc gataactaaa cgaaataaac
      121 gctaaaaccg ctcagaacgc aaaatatgcc attttagagc tattgtagaa aatgtagttt
      181 gaaatgcaat tttcttcttt cagcttttta tttcccactt gtaaatctgc taattatttt
      241 ctaccagaca aaccattgat tttttggcta tcagttaact cacgattatt atgagaaatg
      301 cttgtattct ttgttccctt tttgaacgaa atactaaacc ccaagttaaa cccctccttc
      361 gcgctgtcgc taataaaaag agtgtaaacc tttctgttac tctttgacaa agagtaacat
      421 tttcctaatt gtgacatggc tgtcacaatt ccaaatgctc tccgagggta ttcgctgtca
      481 caagtgacaa cgaaaaaagg agccgaaagc gtgtcacgct ctcaactcct tttacgcttt
      541 attttgcttc acgcaaaata atcgcttatc gtaaactcac gtcattaaac attgacgtaa
      601 atttactctc actcatctga cttttcttat tcggtatcac ttctctgtca cgtccaaacc
      661 caaaagccac gtgtctaatt ctattttcaa gtcgtttgca gattccttaa acgtctctcg
      721 taaatgattc gtcaactcat cgttttggct ttcttctttc aacaatttgc gcaatctata
      781 tttcaaattt ctgctaatat acgcccactc tgaatgatct tgattcagcc cttttatcat
      841 aattctatca acaggtttta catctccagg caagtaatga ggacttgcaa agctatctaa
      901 actttcccga accatcgcat gccaatctgt tgctttgcca cgtcttagct gcatttctat
      961 acgccaccat gtttcgattt cttttggtac aatctgtttt tttcgttcct gttcaagctt
     1021 tttgttgtac atccgcactt gtcgctcgct ggcacgacta ccccagtacg ctgtttctaa
     1081 tttgccagaa cggccataaa ttggcttaaa agacacaggg tcaacgattc gatactgggt
     1141 aataaaatca tcaggaacac cgagaatatc gcaagcaata tctgcacgtg agaaatgcgc
     1201 atccagaaac aaatcatgaa tgaattgttt catcgacccc tttaaaaact cgccaatttt
     1261 atttggatta aaatcaatac gacctttgtc agggtgaaat tttaacattt cgatataggc
     1321 gatatcttct ccatattggt caaataattg ccaaccattt gtaccaaccg acttcaaata
     1381 cccttgattt tcattcaaac gcattaattg ctcaaaatcg acaaacacaa ctccattttg
     1441 cgtccaataa gctatggtat cattcagttt tccgacgatt gtaattcgat cgattgacca
     1501 acttaatttt agggggtgta ccttatcgtc aacacttaac cgcctgttag aaatacggtt
     1561 aagtttttcg agctgattta tcgttgttct tttttctgcc cctcgacctt caatttttga
     1621 ttgaatttca ctcaactgat tttcatttgc cattttcgtc ctccagacga aaaaagagac
     1681 ttttggaaag aatttccaga gttcacgtaa ccctaaaaat tcatatccaa aaatctctag
     1741 cttgaagaaa cctaaaaata ttcgtataat gaacctgagt tacggagcta ggtgaagtag
     1801 tttccgtaaa tagtcgagag tgttagcgca ctgctcggct tttattttgc tcttttttct
     1861 cgttttcttt gattatagca ctcctcctaa aaaaataaaa agacctcagg gaatttcatt
     1921 ccccgaaccc cttgagcctc ctcctgccga aatggaaagg gcgcacccgc tgtttattt
//
