LOCUS       NZ_CP059780             4372 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Enterococcus faecium strain A3895 plasmid pA3895_P8, complete
            sequence.
ACCESSION   NZ_CP059780
VERSION     NZ_CP059780.1
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 4372)
  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  JOURNAL   Unpublished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 4372)
  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 4372)
  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
            CP059780.1.
            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..4372
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A3895"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA3895_P8"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            join(4013..4372,1..3)
                     /locus_tag="HI845_RS15110"
                     /old_locus_tag="H4J14_015105"
     CDS             join(4013..4372,1..3)
                     /locus_tag="HI845_RS15110"
                     /old_locus_tag="H4J14_015105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045135959.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSERDYPDESDDLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            225..1631
                     /locus_tag="HI845_RS15115"
                     /old_locus_tag="H4J14_015110"
     CDS             225..1631
                     /locus_tag="HI845_RS15115"
                     /old_locus_tag="H4J14_015110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_189660795.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSAEMRYIYRQREENEREK
                     ALVASERAEIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     gene            2076..3044
                     /locus_tag="HI845_RS15120"
                     /old_locus_tag="H4J14_015115"
     CDS             2076..3044
                     /locus_tag="HI845_RS15120"
                     /old_locus_tag="H4J14_015115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002347008.1"
                     /translation="MSKKRTIVNEWEKLTALSNRRLNVQTLVQTIKLNWSIDRITIVGK
                     LNQNIFYHTQHDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQHDENIAYIEISKWQE
                     GKGRIDFNPNKISRFLADSMKNFIHDLFLEPHFSRADVACDLIDVPDEFITQYRIIDPV
                     SFKLIYGRSGKLETVYWGSRASERQIRLYNKKIEQEMKRKVVPSEINTWWRLEMQLRRG
                     KATEWYAMVKESLDSFVSPHFLPTDIKPTDKVMIDGLLANHSNWAILSRNSKYKYRNLL
                     KRESQNDELTNHLRETFEESADDLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            3047..3280
                     /locus_tag="HI845_RS15125"
                     /old_locus_tag="H4J14_015120"
     CDS             3047..3280
                     /locus_tag="HI845_RS15125"
                     /old_locus_tag="H4J14_015120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            3273..3692
                     /locus_tag="HI845_RS15130"
                     /old_locus_tag="H4J14_015125"
     CDS             3273..3692
                     /locus_tag="HI845_RS15130"
                     /old_locus_tag="H4J14_015125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            3701..4009
                     /locus_tag="HI845_RS15135"
                     /old_locus_tag="H4J14_015130"
     CDS             3701..4009
                     /locus_tag="HI845_RS15135"
                     /old_locus_tag="H4J14_015130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     Typing          2168..3031
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.264"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          226..1628
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.521"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taagcgatta ttttgcgtga agcaaaataa agcataaaag gagttgatag cgtgacacgc
       61 tttcggctcc ttttttcgtt gtcacttgtg acagcgaaaa ccctcggaga gcgtttggaa
      121 ttgtgacatc catgtcacaa ttaggaaaat gttactcttt gacaaagagt aacagaaagg
      181 tttacaatct ttttattagc gacagcgcga aggagggttt taacttgggg tttagtattt
      241 catttaaaaa aggaacgaag aatacaagta tttctcataa taatcgtgag ttaactgatc
      301 gccagaaaac caatgattgg cataagcaca ttgacttcac gaaatcggat gaaaatattt
      361 atttagagca gacgaatcta gcagataaat atgaggaatt gtttggcgaa gtggtagaaa
      421 aatataatgc gaaacaaaaa agagccgata gaaaaatcga ggactattta gcgaaagtgc
      481 gcaaggataa aaagttggaa cctcaacgag aatttattgt gcaaataggc attttagatg
      541 atttccagac aaatcgagca gatggttctt ctactggcat atcgaaacaa caagctgaac
      601 aaaatcgagt gattgccaat aaaattttgg ttcagtatta caaggagttt caagagagaa
      661 accctaattt ggctgtttat aatgctgtta ttcataatga cgaaataagt ccgcacctgc
      721 acttgaatat tgtgccggtt gctgaaggtt ataaacgggg tgttcaaaag cagccgagct
      781 ttaataaagc actggttcaa caagggatac acgctgataa agataatggt cgagtgcttt
      841 tcaataattt tagaaatcaa gaagttgact ctatagaacg attaatgaat gattacggtt
      901 ggaaaaggga tattgtcggt accaacaaaa ttaaagatat tcacgaatac aaagaaatca
      961 tgagtgaaat ttctgaattg cgccaaacgg ctgtaaaaga gcgtgagagc gtttctgcgg
     1021 aaatgaggta tatttatagg caaagagaag aaaacgagcg tgagaaggct ctggtggctt
     1081 ctgagagagc ggagattgaa gaagagaaga aaaatatgct gaatgtaaaa aaagagatgg
     1141 cggtcatttt ccaaaaagat atggttcctt tagaaagttt caagaggctt cctgatggtt
     1201 cgtatcattt atctgggaat gattttgttg atttgtatca acgagctacg agagcaacaa
     1261 atgccaagag aaatgctgat aacatgagtg agcaatattt acagatgctt gagcaaaata
     1321 cagaattaaa tgagtatgta gctgcattgg aagaagagcg tcatttgtct ggtagaaaac
     1381 aattagcaga tttacaagtg gaaaataaaa agctgaaaga agaaaatcgc tctttacgcc
     1441 agcgtttaga gcgattaaaa aacgcatttc aaaaatcgat cactcgtttg tctatccgtt
     1501 ttggtcttgc agaaaaggat atggggcttt ctgaggaatt agaagtatta gagcaggaga
     1561 aaaccttatt ttatcgtcaa aacgtctcac agcataaatt agagcgttct gagaatgaga
     1621 ttgagtggta gccacgatgt gcagtcaacg gtaccggagg cggtttgtgc cgaggataag
     1681 gagttgacgg ctaaaccact agcccctgaa gctgacattt gctaaaaaat ggcaagtcca
     1741 ttttttggcc aacttagcgt tagcgaagtt tgggggcgcc cttttcaaag ggtgcggttt
     1801 tatttttttg gtatttgcat agctaaagag aagtgctatt attgagttag caaacaaatg
     1861 aactggaaaa agagcaaaaa aataagtcga gcaacgctac caacgttctc gacctttacg
     1921 gaaactaacc acactagttc cgtaactcaa attcattata cgaatatttt taggtttctt
     1981 caagactaga gattgatggt tatgaatttt tagagttacg tgaactctgg aaattctttc
     2041 caaaaatctc ttttttcttt gaggaggaac tgaatatgag taaaaaaaga acaatcgtga
     2101 atgagtggga aaaattaaca gccctgtcta acaggcggtt aaatgttcaa actttggtac
     2161 aaactataaa attaaattgg tcgattgacc gaattaccat tgttggaaag ttgaatcaaa
     2221 atatttttta tcatactcaa catgatgtat taatattaga ttttgaacag cttatgcggg
     2281 taaatgaagg caatggctat ttaaaagcgg ttggaaataa tggttggcag ctattagacc
     2341 aacatgacga aaatattgcc tatattgaaa tttctaaatg gcaagaagga aaagggcgga
     2401 ttgattttaa tcctaataaa atcagtcgat ttttagcgga ttccatgaaa aattttattc
     2461 atgatttatt tttagagccc catttttcac gagcggatgt tgcctgcgat cttattgatg
     2521 tgcctgatga gtttatcacg caatatcgaa ttattgatcc agtttcattt aaattaattt
     2581 atggacgctc aggaaaactg gaaacggtgt attggggtag tcgggcaagc gagcggcaaa
     2641 ttcgtttgta caataaaaaa atagagcaag aaatgaaaag aaaggtggtg ccttcagaaa
     2701 ttaatacttg gtggcggtta gaaatgcagt taagacgtgg taaagctacg gaatggtatg
     2761 ctatggtgaa agaaagtttg gatagctttg tgagtccaca ttttttacca actgatataa
     2821 aacctacgga taaagttatg attgatggat tgttagctaa tcattctaat tgggcgattt
     2881 tgtcaagaaa ctcgaaatat aaatatcgaa atttattaaa gcgagaaagt caaaatgatg
     2941 agttgacgaa tcatttacga gaaacatttg aagaatcagc agatgattta aaaaaagaat
     3001 tggatacttg gttacaggga cttgatgtga cagaggagga atagtaatgg cagaaaaaca
     3061 aaagcatttt ggtaagaaaa attggttggt gaatttaaca ggtgataacg ttgtcgttgt
     3121 ttttttggat agcaaaaaaa tgtccggtaa gttacttgat gtaacgcagt atgagttgat
     3181 tttgaaaaat aataaaattg attccccaat cattatccct aagcatgctg ttaaatatgt
     3241 ttatggggta gctgaaagta acggagaaga taatgactga tttgccagaa aaaatgacca
     3301 taaaaaacct tgctgatgag ttgggtatat ctaaaaatac agtgcgcaat caactggtca
     3361 atgcaggtta tgaccttgct cggtataaag ataatggggt tatcatgtta gacaaggaat
     3421 tgattggtgt tgtgcggtca atttatcggt caaaaggtgg tcaattgact ggtgatttac
     3481 cggtcaatga tgcaggcaat gatttcccgt tagaaaaaga aaatgaattt ttgcgtgaac
     3541 aattagcgga aaaagatagg catatttctg aattaacgga aatgattcgt gaccaacaaa
     3601 aattgacttt gcttcagcaa caaaaaaacg atcagttgtt actagaaaat caagaattaa
     3661 aaaatcgaaa atggtggcaa ttctggaagt gaggtgtgac atggataaaa ttgatttgag
     3721 agaagaaaca gtcgatagaa ttgaattgat gtatgaacgg ttagctgatt atttgaattt
     3781 gccggatgaa gataattata gtgaaatgct tgaacgaatt atggatgttc tcaactcggt
     3841 tatcaatgct gatctagcaa aatcttcagt tttgactaat gaatttgttc ataagcattt
     3901 agcgcaaaca actgatgaat cagaaaaaga attttggttg aaattaatga gtcatgttat
     3961 gcagttaaac caaatttccg ttattaattc caaagaaaag gagatgtagt ttatgggaat
     4021 gactttagca gatattaaag cgcaagaaga aaaattaaaa aaagaacaag cgaaacttcg
     4081 ccaacagaaa aaacgcttga ttgagaaaga aaatgctgca atgggcaagg ctcttcgcaa
     4141 gcgttttggg tttgaaactt ttgctgattt tgagcggtgg ttatcgtcaa tttctgacga
     4201 tcagcaacac gaaaaaacag tggataatga gtggcttgct gatgaaaaat cagcgccaag
     4261 cgaacgagat tatcccgatg aatctgacga cttattcgga gtgataccga ataagaaaag
     4321 tcagatgagt gagagtaaat ttacgtcaat atttaatgac gtgaatttac ga
//
