LOCUS       NZ_CP059821             5212 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain BP657 plasmid pBP657_P5, complete
            sequence.
ACCESSION   NZ_CP059821
VERSION     NZ_CP059821.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675395
            Assembly: GCF_012933075.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5212)
  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  JOURNAL   Unpublished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 5212)
  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 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                     :: BP657
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 44.03x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 06:25:27
            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)                     :: 3,092
            CDSs (total)                      :: 2,999
            Genes (coding)                    :: 2,883
            CDSs (with protein)               :: 2,883
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 38 of 116
            Pseudo Genes (incomplete)         :: 72 of 116
            Pseudo Genes (internal stop)      :: 30 of 116
            Pseudo Genes (multiple problems)  :: 20 of 116
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059821.1.
            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="BP657"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pBP657_P5"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2017"
                     /collected_by="CMC Vellore"
     gene            join(5052..5212,1..340)
                     /locus_tag="HI829_RS15245"
                     /old_locus_tag="HI829_015245"
     CDS             join(5052..5212,1..340)
                     /locus_tag="HI829_RS15245"
                     /old_locus_tag="HI829_015245"
                     /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            313..756
                     /locus_tag="HI829_RS15250"
                     /old_locus_tag="HI829_015250"
     CDS             313..756
                     /locus_tag="HI829_RS15250"
                     /old_locus_tag="HI829_015250"
                     /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            1926..2894
                     /locus_tag="HI829_RS15255"
                     /old_locus_tag="HI829_015255"
     CDS             1926..2894
                     /locus_tag="HI829_RS15255"
                     /old_locus_tag="HI829_015255"
                     /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            2911..3435
                     /locus_tag="HI829_RS15260"
                     /old_locus_tag="HI829_015260"
     CDS             2911..3435
                     /locus_tag="HI829_RS15260"
                     /old_locus_tag="HI829_015260"
                     /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_060800956.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTETHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            3811..4092
                     /locus_tag="HI829_RS15265"
                     /old_locus_tag="HI829_015265"
     CDS             3811..4092
                     /locus_tag="HI829_RS15265"
                     /old_locus_tag="HI829_015265"
                     /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            4094..4510
                     /locus_tag="HI829_RS15270"
                     /old_locus_tag="HI829_015270"
     CDS             4094..4510
                     /locus_tag="HI829_RS15270"
                     /old_locus_tag="HI829_015270"
                     /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          1927..2890
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgaatcaaaa agtcttaatc aagatcaaat aataaaatat gcaaattact gtggtgttta
       61 tcctaaaaaa gtagcacgaa tactaaacct ttcagaggtc caaacacaac taagaaaagg
      121 aaatgccatt tatatgggaa ctgctggtta tggaaattat agtaacagcc gtcatgcact
      181 tgcattattt gggtgggtca atcaaggtgg ttatcaaact tactatgtgt ggaatccttg
      241 gtataactac ccaactgtaa taagtgcaaa tgcaggacca gttacaattc ctgtacctgg
      301 aggtggtttt acttgggaca ataccattac aaattggtaa ataaacccat tgctttagtt
      361 atgggtctag tgttagttct tttcttaact agttgttcaa aaaaacaaga aatacaaaag
      421 actgatctga ttccttttct aggaacttgg caaactaaag atcattcaga acgtctagta
      481 atcactaatt taaatacttc aaaaaatata gaacaatata ccatcttagt aaaagagaac
      541 aatcataaaa ttcaaatcat tgataaaaat ttaaatataa atgaacaagt tttcatttac
      601 aaagcaacaa ataatttact aacactgcgc tctaataaaa aacaattaga ttacactttt
      661 agtttggatt ctccaaaaaa gctcgtattt attttgacaa cgaatgatgg gacagaaggg
      721 acagctaaac caattgaatt ttttaaagct gattgatgaa tagttgtttg atattacaaa
      781 acaataattt caccgaaggt gaaacaagcg aaactttaca aaaagtggct agcatttgct
      841 agcctttttt gtattgtgga gcgtgggttt tgagggggat tcaaggggga gcttgcaccc
      901 ctttgacaag cggttatttg caccaaatac gtaggtattt ggctagcaaa tatagagctt
      961 gccaaacact ttagtgagtt ttgtagaaag tacctttaaa ggtactttca cattacgaac
     1021 gatacgtccg taggacgtac tgaaagggtg ggatttatga gcgaactaat gcaaaatttg
     1081 gctagcaaaa aaagttaaaa aatatatgct aataatcgag cgaaatgaac actttttcaa
     1141 gtgagcgaat ccgccatgac aaagctgaag cagtttattt cagctttgtc atggcgtgtg
     1201 cctagacttt taaaaaagtc ggcacacgag caaatatctt tatcaagctc taatttgcgt
     1261 tttaagacgt ttgaaacgtc taagtatata aatatataag agtaggttta agagtgctta
     1321 aatcgaattt tagagggcat tcagacaact ttagggttgt tagggcttgc cctgaccgcc
     1381 tgtaaggcgc tttaagaaca agataaggga tttatactaa gactgtctta aaacgtctca
     1441 aacgaaggct catagcttct caaagagttc cttatgaaca tttttagcaa aggagccgga
     1501 agcgactgcg cagtataatg tgagagcaga gcgatcacac ctttttaagc gactgtaggg
     1561 agtaagattc ccagttgaga aaaatgcgcg aatctgtttg gagaaaaaag aagtggtttt
     1621 ttaggcggga aattttgtcc ccctctttta taatctcttt ttaaacctct ttttaaacct
     1681 ctttaccgtc ggctatatcc ttactctccc aagggaatga cgcttttatc tacatcgttt
     1741 tgtctgttta tctacatcgt tttgtctgtt tatctacatc gttttgtctg tttatctaca
     1801 tcgttttgtc tgtttgtaca ttgaattagt acatcgacga tgttaatata agatgtagat
     1861 aaacaggcat tttgtatttc ataacgtgta tctcttgtgc gagtaagaaa ggagctattt
     1921 taaatatgtc taatgaaatc gtaaagtatc atcatgaatt aaatacaatt ccgttgcgaa
     1981 aatttacacc agtcgaaatg aatttgttct tttctatcgt atcaagaatg cgtgatgtag
     2041 gtgataaaaa agtacaattt acattcgagc aattaaaaga tttaagcaat tataaagcaa
     2101 ctgcaaatgt tcgattcata gatgatttag aaacaacgta tgacaaatta atggatttac
     2161 gttttggtag aagaagtgct gacggtttgc aacgtgaacg ttttgtttta tttaatcaat
     2221 ttaaaatcga cggaaaatct gatattcctt ttgctgaaat acaagttcat gaaaaagcct
     2281 tacccttact taataatctt gaagaatggg tgcgctattc tctccaacaa ttcaatgaat
     2341 tagaaagcag ttattcaaaa acaatgtttc gattactaaa acaatacaga accaaaggtt
     2401 tcgcttattt ttcaaaagaa gactttcatg aattacttga tattcctaaa agttacaacc
     2461 aaggtacgat tgatcaacgt gtgttcaatc caatacgaca agaactaacc gcaatcttta
     2521 aaggtttaac aatcaaaaag aaatacggaa aaggacgggg aaagcctgtc attggctatc
     2581 aatttacatt taaacctgag ataaaaaaat cagacgactt taacaaacat gccccaacaa
     2641 aagaagaaca aaacaaagca ttagaactag ctaaccaaca agttcaatct gaaaaagcac
     2701 ctacttcatt acaagaaaaa atcaaagaac aaaagcgaaa attggaactt ttacaacagt
     2761 tagaaaagtt agaaagagaa caaaataccc aaaataaaga aaataatgca caaaaatcag
     2821 agataaattc cgatattcct tcagaactaa aaaaagactt attagacaat cttcaaaact
     2881 tattcaaaga ttgaggggtt tttagatttt atgacagaaa aaacaatcaa agaacttgct
     2941 gaagaattag gagttagtaa aacagcaatt aacaaaaaag tttctgacga aaatcgaaaa
     3001 ctttggtttt cgaaaatcgg aaacaagttt gtgattaatg aaaccggaca aaaggctata
     3061 aaatcaatgt tttttaacga aaacgaaaac tcaaatcaac aactagttgg cgaaaaaacg
     3121 aaaaccgaaa cccacaaaaa cgccaaccaa gttcccgaat tagaagtcct ttctctccta
     3181 gaacaacagt taaatcaaaa agatatgcaa ctacaagaaa aagacgagca aataaaacaa
     3241 atgcaaaaat tactcgacca ccaacaacaa ctcaccctgc aagccaacca acaaatcgag
     3301 aaactgcagg aacaactaca gttgacttat acggaagaat cttcggaaaa taaatcaacg
     3361 actctttctg aagaaacaga atcgatagaa aaacaatcaa agacggagaa aaaatggtgg
     3421 caattctggc aataaaacca gcaatttaaa ttaataaaaa ttgctggttt tattcttctt
     3481 tttgcttttg cgagcagagc aacatggacc catgttgcga tattttggtg gcgccccaat
     3541 ccccgttttt tcgttgaatc ttactcggac tgcactcgtt ttacagctga tttttctgaa
     3601 ttttgaaaga gcataaggaa acgtggtatc actttcttac gaaaggtgct agataggctg
     3661 tgcctatcac gtttctcaga aaaaaatttg ctatcacttt tttgccattg tggctaggct
     3721 atgtatagtg ttttggcgaa aaatagctat acaaatacta tatttgtatg gtatacataa
     3781 attatacgct gatacgaaag gaaaatttcc atggacattt tagttcgaaa tatcaatccc
     3841 aaaattattg caagaataga taaacgttgt caggaactca caaccaaaac gggcaaaaaa
     3901 tggagtcgaa ataaatatct aaaagttcta atcgaaagtg attttgaccg tcaacttatg
     3961 aattacaaaa aagatcaatt cgatttatta ctcgaaaaat ttattgccat tcaaacagaa
     4021 aatacgaaca tactgaatga ctatgttcac acaaacaacc aactcattga aacacttatc
     4081 ggaggaatat aacatgagaa aaacttctgt tcaaaaacac gtaacccttt atcccagtca
     4141 cgttgacgtt ttagattcca tcatcgaaaa aaatccagac gtcaacaatt attcagaagc
     4201 cattcgtttt ttatgtatga gttatgaacc tgataccaat acaaccacaa ccagtaacca
     4261 agcaaaactc aatgccatgg gaaaagaaat ttctatcatg acagaaatca tggcagaatt
     4321 tgctgattta tatctaaaag atactggtgt tcttatcggt acaaattcta aagtgtatca
     4381 agaagtgaaa gaaaaaattg aaaatcaact caatccttcc cgacgaaatc aacccaaaaa
     4441 tcgtcaaaaa gaaaccaatc aaacctttac ttctggaaat tttgacccaa caaactttct
     4501 aaaaagataa aaaaagaaac cgatccctaa aaaaattcct cgatttcttt ttagggatca
     4561 gtcttccagc aagatttgca agttggtacc aacttgcgaa aaaaaagaaa aatccgctta
     4621 tgcaacttct tctttttgta ttttggggcg ctaccccaat ccccaagtat cggttattta
     4681 atagcgcgga aatccaaaga ataggacgta ccctgaaaca aaaaaagact gctctcacga
     4741 gcagcccaaa atgagattat cctattcatc aacataaaaa tattacaaag tgaagaacta
     4801 gagaaagaca aaaaaagcat atcaaatcct ctcaaaaata acaagtcttt aaaaaatgac
     4861 agataaaaat gcacaaagaa ctaaaaaaga gaaatcgcgt aaaatcaagc attagaagct
     4921 agtaactagc tagaccaatt aaaaatcaca aagttagcgt ctctatccat tggtagaggg
     4981 gcaacttggc atagtcgaca ttatgttaac tagctcgata aataacgatt atgttcccaa
     5041 aacaatattt tatgaactat aacaaaaatt tgttatcgca tattgtatat tttaattata
     5101 taattatagg tgtataccac ttaaatttaa cacaaaggcg tggttatttt gaaacccaaa
     5161 aagaaaattt atctaggtct cctcttttcc ttgatgattg gaatagtcaa at
//
