LOCUS       NZ_CP059828             4465 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain A15023 plasmid pA15023_P5, complete
            sequence.
ACCESSION   NZ_CP059828
VERSION     NZ_CP059828.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675383
            Assembly: GCF_012933295.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4465)
  AUTHORS   Veeraraghavn,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  JOURNAL   Unpublished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 4465)
  AUTHORS   Veeraraghavn,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 4465)
  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                     :: A15023
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 47.86x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 03:31:11
            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)                     :: 3,055
            CDSs (total)                      :: 2,964
            Genes (coding)                    :: 2,859
            CDSs (with protein)               :: 2,859
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 105
            CDSs (without protein)            :: 105
            Pseudo Genes (ambiguous residues) :: 0 of 105
            Pseudo Genes (frameshifted)       :: 45 of 105
            Pseudo Genes (incomplete)         :: 64 of 105
            Pseudo Genes (internal stop)      :: 33 of 105
            Pseudo Genes (multiple problems)  :: 30 of 105
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059828.1.
            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..4465
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A15023"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA15023_P5"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            join(4101..4465,1..175)
                     /locus_tag="HI843_RS15130"
                     /old_locus_tag="HI843_015130"
     CDS             join(4101..4465,1..175)
                     /locus_tag="HI843_RS15130"
                     /old_locus_tag="HI843_015130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            860..1033
                     /locus_tag="HI843_RS15135"
                     /old_locus_tag="HI843_015135"
     CDS             860..1033
                     /locus_tag="HI843_RS15135"
                     /old_locus_tag="HI843_015135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_010729871.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNGELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            1438..1872
                     /gene="bacA"
                     /locus_tag="HI843_RS15140"
                     /old_locus_tag="HI843_015140"
     CDS             1438..1872
                     /gene="bacA"
                     /locus_tag="HI843_RS15140"
                     /old_locus_tag="HI843_015140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351079.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_169045404.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAAD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     gene            3162..4085
                     /locus_tag="HI843_RS15145"
                     /old_locus_tag="HI843_015145"
     CDS             3162..4085
                     /locus_tag="HI843_RS15145"
                     /old_locus_tag="HI843_015145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     Typing          3163..4085
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctacaagcg aaccaacaaa ttgagaacct acaagaacag ctccatttaa cttatacaga
       61 agaaactcca acaaccgaat caactgcctt ttctgaaaaa aaagcagaca atacacaacc
      121 acttattgaa aaaaagtggt ggcaaatttg gaaatctaat agaaccaatc tctaaaattt
      181 tctagaagtt agttcggata gtagaggaaa aagttgtact acctgatggg gagatcactc
      241 aaatttttat gagaaagaaa aaatagttta caactgtaaa caatcaatgt ttatagttgt
      301 aaactatcaa actatatggt gacttattgc ttaaaatagg ttgaaatctc actcaatttt
      361 tggtggaaaa acaaaataaa ttctaatcga ttttgttgaa aaagtcataa aaaaacaaat
      421 gtgattttaa caaaatttca aaaaaatcgt ttgaaatttc gtttattttt tttgagaatt
      481 ttgatcatcg tagggtcatt gtagaatcat tatgagatca tcgtgggatc atcgaataaa
      541 gtatgggaaa ggcttgcggt gcttggtatt aagggcattc tccgcctccc aggttcttga
      601 ccattttctc tcaacgtggt aaaaatccca cttataagag aaaatggtca agaacctaaa
      661 cggtcggcga agaaaacata ccaagcacca caagcaaaaa aagttagagt aacttccaaa
      721 aaagaaaaat tttttagaac aacttttgaa aatttaattt tgatttatat ccgttcaatt
      781 taaacatttg ataaactgaa ggctagtatt taaaatgtgt atacaagtgg tagcgttaaa
      841 aaaagtggag gtataaccta tgttaaaaaa aactgtgttg gtactgggtt ctatttctct
      901 aggaatatta ggttttagcc ccatgctatt atccgtaatt ggaaaaaaca attccaacgg
      961 agaacttaaa ttaaattcaa attattacaa cagtcctaac gaagaattgt ttgtaaaaga
     1021 gacggataaa taataaaaaa gactgctctt tcgagcagcc agttaaaaaa taatgagtgt
     1081 ttattcttga aaaagcaacg cgcttatgaa gcgctaccaa aaatttatca tattttatga
     1141 aaaataacac cccagtaaaa aatgactggt aaaaattcac aaagaaacgg aaagaagcaa
     1201 ctgcagaaaa tcaagcctta aaaagagctt ttgacttaga ccaatcgaaa atcacaaagt
     1261 gagcccctgt atcccttggt agagaggcta cttggcatag tacacattat gtctactaac
     1321 ctttaaaata acacgtttta taaaataaac cctcttgaca atatttaatt ttctgattat
     1381 tctaaatata tacagaaagc gctttcctag gattttatat ctaaggagga agtaacaatg
     1441 aaaaataaaa ttattaaaat tattacttgt ctatttttgt tcggtatgat tgttggagca
     1501 agtactccgt taaatctgtt tccttttagt gctagaggta taaaagtgga agctgcaagt
     1561 tcacgatata atcataatca tcgtggattt acttgctata aaatgaacta ttatgttact
     1621 aataaaatgt gtagagattt gaaaaaaaat tataataagc taaagactcc tgctcaaatt
     1681 gcatctttta ttcctattgg tggagttgga acatgggtta ttacaaatgc ttttagtagt
     1741 gctgctgatg caatgaatgt ctttgtaaga gctgcaaatc aaggaaaagg tgtacaatta
     1801 acatataatg ctcactttag caatacaaca tcatatcaat acaatgatta cgctcgttat
     1861 gtaataaaat aatcagaaag tgaaactatc tcatgaataa aaagatttta gctgtaatta
     1921 tttcaataat agttttaatc actatgttct tcatatttag gctaattttc aatataagct
     1981 tacaaaaaag tattctttat ctaattccta tagcatttat cttagcaatt tttagaagta
     2041 tttacggaaa taaaaactct aaatagctaa aaataaatca tactaaattt tacaaaaagt
     2101 ggctagcatt ttctagccac tttttgtatt gtggagcgtg ggttttgagg gggattcaag
     2161 ggggagcttg cgcccctttg acaagcggtt atttgcacca aatacggagg tatttggcta
     2221 gcaaatatag agcttgccaa acccttttag tgagttttgt agaaagtacc tttaaaggta
     2281 ctttcacatt acgaacgata cgtccgtagg acgtactgaa agggtgggac ttatgagcaa
     2341 attaatgcaa aatttggcta gcaaaaaagc taaaaaatat atgctaataa tcgagcgaaa
     2401 taaacacttt ttcaagtgag cgaatccgcc atgacaaagc tgaagcagtt tatttcagct
     2461 ttgtcatggc gtgtgccgac ttttttaaaa gtctaggcac acgagcaaat atctttatca
     2521 agctctaatt tgcgttttaa gacgtttgaa acgcctaagt atataaatat ataagaatag
     2581 gtttaagagt gcttaaatcg aattttagag ggcatttaga caattttagg gttgttaggg
     2641 cttgccctga ccgcctgtaa ggcgttttaa gaacaagata agggatttat actaggactg
     2701 tcttaaaatg tcttaaacga acgctcagag cttctcaaag ggttccttat gaacggcttt
     2761 tagcaaagga gccggaggcg actgcgcagt ataatgtgag agcagagcga tcacaccttt
     2821 ttagcgaacc gtagggagca aggtttggaa ttggcagttt tgataaattc gcgaacctgt
     2881 ttagagaaaa aaggagtgat tttttaggcg ggaaaattag cctcccctct ttttatatct
     2941 ctttttatat ctctttttat atctctttta tgtcggctgt gtccttactc tcccaagcaa
     3001 ttcagagttt tttcaagtag gttttctacg cttttcaagt aggttttcta cgcttttcaa
     3061 gtaggttttc tacgcttttc aagtaggttt tccgacatta ttgagtattt ttataaagta
     3121 tgttactttt atttcatact ttataaaagt aggagaagct tatggcaaat gaaattgtaa
     3181 aatatgaaaa tagattaaat catattcctc tgagaaaatt taatagtcgt gaaatgaact
     3241 tatttttttc aattgcttca cgtgtacgtg aaaaaggtgt agatgagatt attttttcat
     3301 ttcacgattt gaaaaaacta agcggttata cagaacgtgg ggaacaattt ataaaagatc
     3361 ttagtagcac gtatgacaaa ttattaagta ttaatgcttg gaatgatgat ggaaatactt
     3421 taactaaatt tgttgctttc acaaaatata gcattatacg agataaacaa cttgttataa
     3481 tttcagttaa tccagaattt aaaggacttt ttaatcaatt aaagaactgg acaagattta
     3541 atctagagca atttactaat ttggatagca catattcaaa aactatgttt cgattattaa
     3601 aacaatatcg aactcaaggc tggactgaat tttccaaaga aaaatttttt gatttactag
     3661 atattcctaa aagttattgg aatagtccgt caaatattga caaatttatc ttaaggccaa
     3721 ttaaagaaga actcactccc ttatttaaag gattaactat tcgtaaaaaa tatggtaaag
     3781 gtcgaggtaa acctgttatc ggttatcgtt ttacttggaa agctgaaatt aaccatgctg
     3841 acgatttttc caaagggaaa caagaagatt tacgtataaa attatttaat attgatcaca
     3901 atggagaatt aacacgagaa gaaaaatggc gcgctaaaga tcgaatacta aatcttccct
     3961 taggcactca tgaagctgat tttaaacaac aacaacaaac tgaagaaaaa caggcagaaa
     4021 aacgagaact ttcaaacaaa ctcaaacaag atttactagg aaatttacaa aacttattcg
     4081 attaagctta aggagtattt atggcagata aaacaatcaa agaacttgcg gaagaattag
     4141 gagttagtaa aacagcaatt aacaaaaaag tttctgacaa aaatcgaaaa ctttggtttg
     4201 caaaaaacgg aaacaagttt gtgattaacg aaaccggtca aaaagctata aaatcaatgt
     4261 ttttagtcga taacgcaaac ttaaatcgaa aactagttgg cgaaaaatca aaaaccaaaa
     4321 accataaaaa caccaaccaa gtttccgaat taaaactcct ttctttccta gaaaaacagt
     4381 taaatcgaaa agatatacag ctacaagaaa aagataatca aataaaacaa atgcaaaaat
     4441 tactcgacca gcaacaacaa ctcac
//
