LOCUS       NZ_CP059761             4372 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain A10290 plasmid pA10290_P6, complete
            sequence.
ACCESSION   NZ_CP059761
VERSION     NZ_CP059761.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675380
            Assembly: GCF_012933345.2
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  JOURNAL   Unpublished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                     :: A10290
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.54x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 03:59:25
            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)                     :: 3,199
            CDSs (total)                      :: 3,107
            Genes (coding)                    :: 2,958
            CDSs (with protein)               :: 2,958
            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)              :: 149
            CDSs (without protein)            :: 149
            Pseudo Genes (ambiguous residues) :: 0 of 149
            Pseudo Genes (frameshifted)       :: 48 of 149
            Pseudo Genes (incomplete)         :: 96 of 149
            Pseudo Genes (internal stop)      :: 34 of 149
            Pseudo Genes (multiple problems)  :: 26 of 149
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059761.1.
            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="A10290"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA10290_P6"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            join(3957..4372,1..991)
                     /locus_tag="HI839_RS15825"
                     /old_locus_tag="HI839_015820"
     CDS             join(3957..4372,1..991)
                     /locus_tag="HI839_RS15825"
                     /old_locus_tag="HI839_015820"
                     /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_060810507.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     gene            1436..2404
                     /locus_tag="HI839_RS15830"
                     /old_locus_tag="HI839_015825"
     CDS             1436..2404
                     /locus_tag="HI839_RS15830"
                     /old_locus_tag="HI839_015825"
                     /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            2407..2640
                     /locus_tag="HI839_RS15835"
                     /old_locus_tag="HI839_015830"
     CDS             2407..2640
                     /locus_tag="HI839_RS15835"
                     /old_locus_tag="HI839_015830"
                     /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            2633..3052
                     /locus_tag="HI839_RS15840"
                     /old_locus_tag="HI839_015835"
     CDS             2633..3052
                     /locus_tag="HI839_RS15840"
                     /old_locus_tag="HI839_015835"
                     /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            3061..3369
                     /locus_tag="HI839_RS15845"
                     /old_locus_tag="HI839_015840"
     CDS             3061..3369
                     /locus_tag="HI839_RS15845"
                     /old_locus_tag="HI839_015840"
                     /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"
     gene            3373..3735
                     /locus_tag="HI839_RS15850"
                     /old_locus_tag="HI839_015845"
     CDS             3373..3735
                     /locus_tag="HI839_RS15850"
                     /old_locus_tag="HI839_015845"
                     /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"
     Typing          1528..2391
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.264"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          3..988
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.617"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3865..4370
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.408"
                     /coverage="99.0"
                     /evalue="4.13e-104"
ORIGIN
        1 caaggagttt caagagagaa accctaattt ggctgtttat aatgctgtta ttcataatga
       61 cgaaataagt ccgcacctgc acttgaatat tgtgccggtt gctgaaggtt ataaacgggg
      121 tgttcaaaag cagccgagct ttaataaagc actggttcaa caagggatac acgctgataa
      181 agataatggt cgagtgcttt tcaataattt tagaaatcaa gaagttgact ctatagaacg
      241 attaatgaat gattacggtt ggaaaaggga tattgtcggt accaacaaaa ttaaagatat
      301 tcacgaatac aaagaaatca tgagtgaaat ttctgaattg cgccaaacgg ctgtaaaaga
      361 gcgtgagagc gtttctgatg agttgaggta tatttatagg caaagagaag aaaacgagcg
      421 tgataaggct ctgatggctt ctgagagagc gaagattgaa gaagagaaga aaaatatgct
      481 gaatgtaaaa aaagagatgg cggtcatttt ccaaaaagat atggttcctt tagaaagttt
      541 caagaggctt cctgatggtt cgtatcattt atctgggaat gattttgttg atttgtatca
      601 acgagctacg agagcaacaa atgccaagag aaatgctgat aacatgagtg agcaatattt
      661 acagatgctt gagcaaaata cagaattaaa tgagtatgta gctacattgg aagaagagcg
      721 tcatttgtct ggtagaaaac aattagcaga tttacaagtg gaaaataaaa agctgaaaga
      781 agaaaatcgc tctttacgcc agcgtttaga gcgattaaaa aacgcatttc aaaaatcgat
      841 cactcgtttg tctatccgtt ttggtcttgc agaaaaggat atggggcttt ctgaggaatt
      901 agaagtatta gagcaggaga aaaccttatt ttatcgtcaa aacgtctcac agcataaatt
      961 agagcgttct gagaatgaga ttgagtggta gccacgatgt gcagtcaacg gtaccggagg
     1021 cggtttgtgc cgaggataag gagttgacgg ctaaaccact agcccctgaa gctgacattt
     1081 gctaaaaaat ggcaagtcca ttttttggcc aacttagcgt tagcgaagtt tgggggcgcc
     1141 cttttcaaag ggtgcggttt tatttttttg gtatttgcat agctaaagag aagtgctatt
     1201 attgagttag caaacaaatg aactggaaaa agagcaaaaa aataagtcga gcaacgctac
     1261 caacgttctc gacctttacg gaaactaacc acactagttc cgtaactcaa attcattata
     1321 cgaatatttt taggtttctt caagactaga gattgatggt tatgaatttt tagagttacg
     1381 tgaactctgg aaattctttc caaaaatctc ttttttcttt gaggaggaac tgaatatgag
     1441 taaaaaaaga acaatcgtga atgagtggga aaaattaaca gccctgtcta acaggcggtt
     1501 aaatgttcaa actttggtac aaactataaa attaaattgg tcgattgacc gaattaccat
     1561 tgttggaaag ttgaatcaaa atatttttta tcatactcaa catgatgtat taatattaga
     1621 ttttgaacag cttatgcggg taaatgaagg caatggctat ttaaaagcgg ttggaaataa
     1681 tggttggcag ctattagacc aacatgacga aaatattgcc tatattgaaa tttctaaatg
     1741 gcaagaagga aaagggcgga ttgattttaa tcctaataaa atcagtcgat ttttagcgga
     1801 ttccatgaaa aattttattc atgatttatt tttagagccc catttttcac gagcggatgt
     1861 tgcctgcgat cttattgatg tgcctgatga gtttatcacg caatatcgaa ttattgatcc
     1921 agtttcattt aaattaattt atggacgctc aggaaaactg gaaacggtgt attggggtag
     1981 tcgggcaagc gagcggcaaa ttcgtttgta caataaaaaa atagagcaag aaatgaaaag
     2041 aaaggtggtg ccttcagaaa ttaatacttg gtggcggtta gaaatgcagt taagacgtgg
     2101 taaagctacg gaatggtatg ctatggtgaa agaaagtttg gatagctttg tgagtccaca
     2161 ttttttacca actgatataa aacctacgga taaagttatg attgatggat tgttagctaa
     2221 tcattctaat tgggcgattt tgtcaagaaa ctcgaaatat aaatatcgaa atttattaaa
     2281 gcgagaaagt caaaatgatg agttgacgaa tcatttacga gaaacatttg aagaatcagc
     2341 agatgattta aaaaaagaat tggatacttg gttacaggga cttgatgtga cagaggagga
     2401 atagtaatgg cagaaaaaca aaagcatttt ggtaagaaaa attggttggt gaatttaaca
     2461 ggtgataacg ttgtcgttgt ttttttggat agcaaaaaaa tgtccggtaa gttacttgat
     2521 gtaacgcagt atgagttgat tttgaaaaat aataaaattg attccccaat cattatccct
     2581 aagcatgctg ttaaatatgt ttatggggta gctgaaagta acggagaaga taatgactga
     2641 tttgccagaa aaaatgacca taaaaaacct tgctgatgag ttgggtatat ctaaaaatac
     2701 agtgcgcaat caactggtca atgcaggtta tgaccttgct cggtataaag ataatggggt
     2761 tatcatgtta gacaaggaat tgattggtgt tgtgcggtca atttatcggt caaaaggtgg
     2821 tcaattgact ggtgatttac cggtcaatga tgcaggcaat gatttcccgt tagaaaaaga
     2881 aaatgaattt ttgcgtgaac aattagcgga aaaagatagg catatttctg aattaacgga
     2941 aatgattcgt gaccaacaaa aattgacttt gcttcagcaa caaaaaaacg atcagttgtt
     3001 actagaaaat caagaattaa aaaatcgaaa atggtggcaa ttctggaagt gaggtgtgac
     3061 atggataaaa ttgatttgag agaagaaaca gtcgatagaa ttgaattgat gtatgaacgg
     3121 ttagctgatt atttgaattt gccggatgaa gataattata gtgaaatgct tgaacgaatt
     3181 atggatgttc tcaactcggt tatcaatgct gatctagcaa aatcttcagt tttgactaat
     3241 gaatttgttc ataagcattt agcgcaaaca actgatgaat cagaaaaaga attttggttg
     3301 aaattaatga gtcatgttat gcagttaaac caaatttccg ttattaattc caaagaaaag
     3361 gagatgtagt ttatgggaat gactttagca gatattaaag cgcaagaaga aaaattaaaa
     3421 aaagaacaag cgaaacttcg ccaacagaaa aaacgcttga ttgagaaaga aaatgctgca
     3481 atgggcaagg ctcttcgcaa gcgttttggg tttgaaactt ttgctgattt tgagcggtgg
     3541 ttatcgtcaa tttctgacga tcagcaacac gaaaaaacag tggataatga gtggcttgct
     3601 gatgaaaaat cagcgccaag cgaacgagat tatcccgatg aatctgacga cttattcgga
     3661 gtgataccga ataagaaaag tcagatgagt gagagtaaat ttacgtcaat atttaatgac
     3721 gtgaatttac gataagcgat tattttgcgt gaagcaaaat aaagcataaa aggagttgat
     3781 agcgtgatac gctttcggct ccttttttcg ttgtcacttg tgacagcgaa aaccctcgga
     3841 gagcgtttgg aattgtgaca tccatgtcac aattaggaaa atgttactct ttgacaaaga
     3901 gtaacataaa ggtttacaat ctttttatta gcgacagcgc gaaggagggt tttaacttgg
     3961 ggtttagtat ttcatttaaa aaaggaacga agaatacaag tatttctcat aataatcgtg
     4021 agttaactga tcgccagaaa accaatgatt ggcataagca cattgacttc acgaaatcgg
     4081 atgaaaatat ttatttagag cagacgaatc tagcagataa atatgaggaa ttgtttggcg
     4141 aagtggtaga aaaatataat gcgaaacaaa aaagagccga tagaaaaatc gaggactatt
     4201 tagcgaaagt gcgcaaggat aaaaagttgg aacctcaacg agaatttatt gtgcaaatag
     4261 gcattttaga tgatttccag acaaatcgag cagatggttc ttctactggc atatcgaaac
     4321 aacaagctga acaaaatcga gtgattgcca ataaaatttt ggttcagtat ta
//
