LOCUS       NZ_CP059802             5212 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain BP3378 plasmid pBP3378_P9, complete
            sequence.
ACCESSION   NZ_CP059802
VERSION     NZ_CP059802.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675393
            Assembly: GCF_012933055.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5212)
  AUTHORS   Veeraraghavan,B.
  TITLE     Complete genome of vancomycin resistant Enterococcus faecium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5212)
  AUTHORS   Veeraraghavan,B.
  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 5212)
  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                     :: BP3378
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 42.82x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 03:40:36
            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)                     :: 3,196
            CDSs (total)                      :: 3,103
            Genes (coding)                    :: 2,981
            CDSs (with protein)               :: 2,981
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 40 of 122
            Pseudo Genes (incomplete)         :: 74 of 122
            Pseudo Genes (internal stop)      :: 28 of 122
            Pseudo Genes (multiple problems)  :: 17 of 122
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059802.1.
            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..5212
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BP3378"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pBP3378_P9"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(join(5063..5212,1..132))
                     /locus_tag="HI838_RS15795"
                     /old_locus_tag="HI838_015795"
     CDS             complement(join(5063..5212,1..132))
                     /locus_tag="HI838_RS15795"
                     /old_locus_tag="HI838_015795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            complement(508..1032)
                     /locus_tag="HI838_RS15800"
                     /old_locus_tag="HI838_015800"
     CDS             complement(508..1032)
                     /locus_tag="HI838_RS15800"
                     /old_locus_tag="HI838_015800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /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_169053707.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTETHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDPQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(1049..2017)
                     /locus_tag="HI838_RS15805"
                     /old_locus_tag="HI838_015805"
     CDS             complement(1049..2017)
                     /locus_tag="HI838_RS15805"
                     /old_locus_tag="HI838_015805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            complement(3187..3630)
                     /locus_tag="HI838_RS15810"
                     /old_locus_tag="HI838_015810"
     CDS             complement(3187..3630)
                     /locus_tag="HI838_RS15810"
                     /old_locus_tag="HI838_015810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318191.1"
                     /translation="MGQYHYKLVNKPIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     gene            complement(3603..4103)
                     /locus_tag="HI838_RS15815"
                     /old_locus_tag="HI838_015815"
     CDS             complement(3603..4103)
                     /locus_tag="HI838_RS15815"
                     /old_locus_tag="HI838_015815"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060800863.1"
                     /translation="MNYNKNLLSHIVYFNYIIIGVYHLNLTQRRGYFETQKENLSRSPL
                     FLDDWNSQIESKSLNQDQIIKYANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGY
                     GNYSNSRHALALFGWVNQGGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTI
                     TNW"
                     /name="hypothetical protein"
     gene            complement(4645..5061)
                     /locus_tag="HI838_RS15820"
                     /old_locus_tag="HI838_015820"
     CDS             complement(4645..5061)
                     /locus_tag="HI838_RS15820"
                     /old_locus_tag="HI838_015820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     Typing          complement(1054..2017)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atcactttcg attagaactt ttagatattt atttcgactc cattttttgc ccgttttggt
       61 tgtgagttcc tgacaacgtt tatctattct tgcaataatt ttgggattga tatttcgaac
      121 taaaatgtcc atggaaattt tcctttcgta tcagcgtata atttatgtat accatacaaa
      181 tatagtattt gtatagctat ttttcgccaa aacactatac atagcctagc cacaatggca
      241 aaaaagtgat agcaaatttt tttctgagaa acgtgatagg cacagcctat ctagcacctt
      301 tcgtaagaaa gtgataccac gtttccttat gctctttcaa aattcagaaa aatcagctgt
      361 aaaacgagtg cagtccgagt aagattcaac gaaaaaacgg ggattggggc gccaccaaaa
      421 tatcgcaaca tgggtccatg ttgctctgct cgcaaaagca aaaagaagaa taaaaccagc
      481 aatttttatt aatttaaatt gctggtttta ttgccagaat tgccaccatt ttttctccgt
      541 ctttgattgt ttttctatcg attctgtttc ttcagaaaga gtcgttgatt tattttccga
      601 agattcttcc gtataagtca actgtagttg ttcctgcagt ttctcgattt gttggttggc
      661 ttgcagggtg agttgttgtt gggggtcgag taatttttgc atttgtttta tttgctcgtc
      721 tttttcttgt agttgcatat ctttttgatt taactgttgt tctaggagag aaaggacttc
      781 taattcggga acttggttgg cgtttttgtg ggtttcggtt ttcgtttttt cgccaactag
      841 ttgttgattt gagttttcgt tttcgttaaa aaacattgat tttatagcct tttgtccggt
      901 ttcattaatc acaaacttgt ttccgatttt cgaaaaccaa agttttcgat tttcgtcaga
      961 aacttttttg ttaattgctg ttttactaac tcctaattct tcagcaagtt ctttgattgt
     1021 tttttctgtc ataaaatcta aaaacccctc aatctttgaa taagttttga agattgtcta
     1081 ataagtcttt ttttagttct gaaggaatat cggaatttat ctctgatttt tgtgcattat
     1141 tttctttatt ttgggtattt tgttctcttt ctaacttttc taactgttgt aaaagttcca
     1201 attttcgctt ttgttctttg attttttctt gtaatgaagt aggtgctttt tcagattgaa
     1261 cttgttggtt agctagttct aatgctttgt tttgttcttc ttttgttggg gcatgtttgt
     1321 taaagtcgtc tgattttttt atctcaggtt taaatgtaaa ttgatagcca atgacaggct
     1381 ttccccgtcc ttttccgtat ttctttttga ttgttaaacc tttaaagatt gcggttagtt
     1441 cttgtcgtat tggattgaac acacgttgat caatcgtacc ttggttgtaa cttttaggaa
     1501 tatcaagtaa ttcatgaaag tcttcttttg aaaaataagc gaaacctttg gttctgtatt
     1561 gttttagtaa tcgaaacatt gtttttgaat aactgctttc taattcattg aattgttgga
     1621 gagaatagcg cacccattct tcaagattat taagtaaggg taaggctttt tcatgaactt
     1681 gtatttcagc aaaaggaata tcagattttc cgtcgatttt aaattgatta aataaaacaa
     1741 aacgttcacg ttgcaaaccg tcagcacttc ttctaccaaa acgtaaatcc attaatttgt
     1801 catacgttgt ttctaaatca tctatgaatc gaacatttgc agttgcttta taattgctta
     1861 aatcttttaa ttgctcgaat gtaaattgta cttttttatc acctacatca cgcattcttg
     1921 atacgataga aaagaacaaa ttcatttcga ctggtgtaaa ttttcgcaac ggaattgtat
     1981 ttaattcatg atgatacttt acgatttcat tagacatatt taaaatagct cctttcttac
     2041 tcgcacaaga gatacacgtt atgaaataca aaatgcctgt ttatctacat cttatattaa
     2101 catcgtcgat gtactaattc aatgtacaaa cagacaaaac gatgtagata aacagacaaa
     2161 acgatgtaga taaacagaca aaacgatgta gataaacaga caaaacgatg tagataaaag
     2221 cgtcattccc ttgggagagt aaggatatag ccgacggtaa agaggtttaa aaagaggttt
     2281 aaaaagagat tataaaagag ggggacaaaa tttcccgcct aaaaaaccac ttcttttttc
     2341 tccaaacaga ttcgcgcatt tttctcaact gggaatctta ctccctacag tcgcttaaaa
     2401 aggtgtgatc gctctgctct cacattatac tgcgcagtcg cttccggctc ctttgctaaa
     2461 aatgttcata aggaactctt tgagaagcta tgagccttcg tttgagacgt tttaagacag
     2521 tcttagtata aatcccttat cttgttctta aagcgcctta caggcggtca gggcaagccc
     2581 taacaaccct aaagttgtct gaatgccctc taaaattcga tttaagcact cttaaaccta
     2641 ctcttatata tttatatact tagacgtttc aaacgtctta aaacgcaaat tagagcttga
     2701 taaagatatt tgctcgtgtg ccgacttttt taaaagtcta ggcacacgcc atgacaaagc
     2761 tgaaataaac tgcttcagct ttgtcatggc ggattcgctc acttgaaaaa gtgttcattt
     2821 cgctcgatta ttagcatata ttttttaact ttttttgcta gccaaatttt gcattagttc
     2881 gctcataaat cccacccttt cagtacgtcc tacggacgta tcgttcgtaa tgtgaaagta
     2941 cctttaaagg tactttctac aaaactcact aaagtgtttg gcaagctcta tatttgctag
     3001 ccaaatacct acgtatttgg tgcaaataac cgcttgtcaa aggggtgcaa gctccccctt
     3061 gaatccccct caaaaaccac gctccacaat acaaaaaagg ctagcaaatg ctagccactt
     3121 tttgtaaagt ttcgcttgtt tcaccttcgg tgaaattatt gttttgtaat atcaaacaac
     3181 tattcatcaa tcagctttaa aaaattcaat tggtttagct gtcccttctg tcccatcatt
     3241 cgttgtcaaa ataaatacga gcttttttgg agaatccaaa ctaaaagtgt aatctaattg
     3301 ttttttatta gagcgcagtg ttagtaaatt atttgttgct ttgtaaatga aaacttgttc
     3361 atttatattt aaatttttat caatgatttg aattttatga ttgttctctt ttactaagat
     3421 ggtatattgt tctatatttt ttgaagtatt taaattagtg attactagac gttctgaatg
     3481 atctttagtt tgccaagttc ctagaaaagg aatcagatca gtcttttgta tttcttgttt
     3541 ttttgaacaa ctagttaaga aaagaactaa cactagaccc ataactaaag caatgggttt
     3601 atttaccaat ttgtaatggt attgtcccaa gtaaaaccac ctccaggtac aggaattgta
     3661 actggtcctg catttgcact tattacagtt gggtagttat accaaggatt ccacacatag
     3721 taagtttgat aaccaccttg attgacccac ccaaataatg caagtgcatg acggctgtta
     3781 ctataatttc cataaccagc agttcccata taaatggcat ttccttttct tagttgtgtt
     3841 tggacctctg aaaggtttag tattcgtgct acttttttag gataaacacc acagtaattt
     3901 gcatatttta ttatttgatc ttgattaaga ctttttgatt caatttgact attccaatca
     3961 tcaaggaaaa gaggagacct agataaattt tctttttggg tttcaaaata accacgcctt
     4021 tgtgttaaat ttaagtggta tacacctata attatataat taaaatatac aatatgcgat
     4081 aacaaatttt tgttatagtt cataaaatat tgttttggga acataatcgt tatttatcga
     4141 gctagttaac ataatgtcga ctatgccaag ttgcccctct accaatggat agagacgcta
     4201 actttgtgat ttttaattgg tctagctagt tactagcttc taatgcttga ttttacgcga
     4261 tttctctttt ttagttcttt gtgcattttt atctgtcatt ttttaaagac ttgttatttt
     4321 tgagaggatt tgatatgctt tttttgtctt tctctagttc ttcactttgt aatattttta
     4381 tgttgatgaa taggataatc tcattttggg ctgctcgtga gagcagtctt tttttgtttc
     4441 agggtacgtc ctattctttg gatttccgcg ctattaaata accgatactt ggggattggg
     4501 gtagcgcccc aaaatacaaa aagaagaagt tgcataagcg gatttttctt ttttttcgca
     4561 agttggtacc aacttgcaaa tcttgctgga agactgatcc ctaaaaagaa atcgaggaat
     4621 ttttttaggg atcggtttct ttttttatct ttttagaaag tttgttgggt caaaatttcc
     4681 agaagtaaag gtttgattgg tttctttttg acgatttttg ggttgatttc gtcgggaagg
     4741 attgagttga ttttcaattt tttctttcac ttcttgatac actttagaat ttgtaccgat
     4801 aagaacacca gtatctttta gatataaatc agcaaattct gccatgattt ctgtcatgat
     4861 agaaatttct tttcccatgg cattgagttt tgcttggtta ctggttgtgg ttgtattggt
     4921 atcaggttca taactcatac ataaaaaacg aatggcttct gaataattgt tgacgtctgg
     4981 atttttttcg atgatggaat ctaaaacgtc aacgtgactg ggataaaggg ttacgtgttt
     5041 ttgaacagaa gtttttctca tgttatattc ctccgataag tgtttcaatg agttggttgt
     5101 ttgtgtgaac atagtcattc agtatgttcg tattttctgt ttgaatggca ataaattttt
     5161 cgagtaataa atcgaattga tcttttttgt aattcataag ttgacggtca aa
//
