LOCUS       NZ_CP059783             1928 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Enterococcus faecium strain A3895 plasmid pA3895_P11, complete
            sequence.
ACCESSION   NZ_CP059783
VERSION     NZ_CP059783.1
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 1928)
  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  JOURNAL   Unpublished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 1928)
  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 1928)
  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
            CP059783.1.
            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..1928
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A3895"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA3895_P11"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(<237..419)
                     /locus_tag="HI845_RS15170"
                     /old_locus_tag="H4J14_015165"
                     /pseudo=""
     CDS             complement(<237..419)
                     /locus_tag="HI845_RS15170"
                     /old_locus_tag="H4J14_015165"
                     /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(619..1584)
                     /locus_tag="HI845_RS15175"
                     /old_locus_tag="H4J14_015170"
     CDS             complement(619..1584)
                     /locus_tag="HI845_RS15175"
                     /old_locus_tag="H4J14_015170"
                     /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_010861627.1"
                     /translation="MSKKGIIVNEWEKLNRISNRRLNVQNLNTPLKLQWSIDRITIVGK
                     LKENIYYHTPNDVLILNFEQLMQLNEGNGFVKSVGKNGWQIVDQYEENIAYIELLQFHE
                     GKARIDFNPNKIGQFLASSMKNFIHDLFLEPHFSRADIACDMVNVPDEFIMQYRVVDPV
                     SFKPIYGRSGKLESAYWGSRASERQIRLYNKKLEQETKRKVVPKEVETWWRLEMQLRRG
                     KATDWHNMVQESLNSFASLHFLPIDTTPTDRIMLAGLMSDQNFWSLLSRNSKYKYRELL
                     KEESQNDELTNHLRETFAESADNLKQELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(673..1506)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.526"
                     /coverage="92.0"
                     /evalue="1.34e-180"
ORIGIN
        1 cacaatctaa cacgaccgtt ccgctaccag tcgccttaca ggctccattt tcgctcctct
       61 aacgtgtttc accgattgtg ccgataacta aacgaaataa acgctaaaac cgctcagaac
      121 gcaaaatatg ccattttaga gttattgtag aaaatgtagt ttgaaatgca attttcttct
      181 ttcagctttt tatttcccac ttgtaaatct gctaattatt ttctaccaga caaactatta
      241 attttttggc tatcagttaa ctcacgatta ttatgagaaa tgcttgtatt ttttgttccc
      301 tttttgaacg aaatactaaa ccccaagtta aacccctcct tcgcgctgtc gctaataaaa
      361 agagtgtaaa cctttctgtt actctttgac aaagagtaac attttcctaa ttgtgacatg
      421 gctgtcacaa ttccaaatgc tctccgaggg tattcgctgt cacaagtgac aacgaaaaaa
      481 ggagccgaaa gcgtgtcacg ctctcaactc cttttacgct ttattttgct tcacgcaaaa
      541 taatcgctta tcgtaaactc acgtcattaa acattgacgt aaatttactc tcactcatct
      601 gacttttctt attcggtatc acttctctgt cacgtccaaa cccaaaagcc acgtgtctaa
      661 ttcttgtttc aaattgtctg ccgattctgc aaacgtttct cgcaaatgat tcgtcaattc
      721 atcattttga ctttcttctt tcagcaattc ccgatattta tattttgaat tcctcgacaa
      781 aagagaccag aaattttgat cagacattaa accagcgagc attattctat ctgtaggtgt
      841 tgtatcaatc ggcaaaaaat gcaggctcgc aaaactattc aaactttctt gaaccatatt
      901 atgccaatcg gttgccttgc cacgccgtag ttgcatttct aaccgccacc aagtctcaac
      961 ttcctttggt acaacttttc gtttggtttc ttgttccaat tttttattgt atagccgaat
     1021 ttgtcgttcg ctggcacggc taccccaata agctgattct agttttccag aacgcccgta
     1081 aatcggtttg aacgataccg ggtcaaccac acgatattgc ataataaact catccggaac
     1141 attaaccata tcgcaagcga tatctgcccg cgaaaaatgg ggttctaaaa acaaatcatg
     1201 aatgaaattt ttcatcgaac tggctaaaaa ctgaccaatt ttattgggat taaaatcaat
     1261 tcgtgctttc ccttcatgaa attgcaagag ctcaatatac gcgatatttt cttcgtattg
     1321 gtcgacaatt tgccagccat ttttaccaac tgatttgaca aacccattcc cctcattcaa
     1381 ttgcatcaat tgctcaaaat ttaaaatcaa gacatcattt ggtgtgtgat aataaatatt
     1441 ttctttcaat tttccaacaa tggtaattcg gtcgattgac cactgtaatt ttaggggggt
     1501 gttcaaattt tgaacattta accgcctgtt agaaatacgg ttaagttttt cccactcatt
     1561 tacgattatg ccttttttac tcaaaaatag ctcctcctca acgaaaaaag agattcttgg
     1621 aaagaatttc cagagttcac gtaactctaa aaatccacat ccaaaaatct ctagcttgaa
     1681 gaaacctaaa aatattcgta taatgaactt gagttacgga actaggtgaa gtagtttccg
     1741 taaaggtcga gagtgcgtca acactgctcg actatttttt tactcttttt tctcattttc
     1801 tttgattata gcactcctct agaaaaaata aaaagacctc agggaatttc attccccgaa
     1861 ccccttgagc ctcctcctgc cgaaatagaa tggcgctgcc agcatttatt tcgttcagct
     1921 atcggcta
//
