LOCUS       NZ_CP059745             5212 bp    DNA     circular CON 01-OCT-2023
DEFINITION  Enterococcus faecium strain A4694 plasmid pA4694_P6, complete
            sequence.
ACCESSION   NZ_CP059745
VERSION     NZ_CP059745.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675385
            Assembly: GCF_012933245.2
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  JOURNAL   Unpublished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                     :: A4694
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 91.24x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/01/2023 03:42:29
            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)                     :: 3,020
            CDSs (total)                      :: 2,928
            Genes (coding)                    :: 2,815
            CDSs (with protein)               :: 2,815
            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)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 38 of 113
            Pseudo Genes (incomplete)         :: 69 of 113
            Pseudo Genes (internal stop)      :: 30 of 113
            Pseudo Genes (multiple problems)  :: 20 of 113
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059745.1.
            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="A4694"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA4694_P6"
                     /geo_loc_name="India:Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(1029..1472)
                     /locus_tag="HI848_RS14885"
                     /old_locus_tag="H4J15_014885"
     CDS             complement(1029..1472)
                     /locus_tag="HI848_RS14885"
                     /old_locus_tag="H4J15_014885"
                     /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(1445..1945)
                     /locus_tag="HI848_RS14890"
                     /old_locus_tag="H4J15_014890"
     CDS             complement(1445..1945)
                     /locus_tag="HI848_RS14890"
                     /old_locus_tag="H4J15_014890"
                     /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(2487..2903)
                     /locus_tag="HI848_RS14895"
                     /old_locus_tag="H4J15_014895"
     CDS             complement(2487..2903)
                     /locus_tag="HI848_RS14895"
                     /old_locus_tag="H4J15_014895"
                     /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"
     gene            complement(2905..3186)
                     /locus_tag="HI848_RS14900"
                     /old_locus_tag="H4J15_014900"
     CDS             complement(2905..3186)
                     /locus_tag="HI848_RS14900"
                     /old_locus_tag="H4J15_014900"
                     /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(3562..4086)
                     /locus_tag="HI848_RS14905"
                     /old_locus_tag="H4J15_014905"
     CDS             complement(3562..4086)
                     /locus_tag="HI848_RS14905"
                     /old_locus_tag="H4J15_014905"
                     /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            complement(4103..5071)
                     /locus_tag="HI848_RS14910"
                     /old_locus_tag="H4J15_014910"
     CDS             complement(4103..5071)
                     /locus_tag="HI848_RS14910"
                     /old_locus_tag="H4J15_014910"
                     /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"
     Typing          complement(4108..5071)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaacgatgta gataaacaga caaaacgatg tagataaaca gacaaaacga tgtagataaa
       61 agcgtcattc ccttgggaga gtaaggatat agccgacggt aaagaggttt aaaaagaggt
      121 ttaaaaagag attataaaag agggggacaa aatttcccgc ctaaaaaacc acttcttttt
      181 tctccaaaca gattcgcgca tttttctcaa ctgggaatct tactccctac agtcgcttaa
      241 aaaggtgtga tcgctctgct ctcacattat actgcgcagt cgcttccggc tcctttgcta
      301 aaaatgttca taaggaactc tttgagaagc tatgagcctt cgtttgagac gttttaagac
      361 agtcttagta taaatccctt atcttgttct taaagcgcct tacaggcggt cagggcaagc
      421 cctaacaacc ctaaagttgt ctgaatgccc tctaaaattc gatttaagca ctcttaaacc
      481 tactcttata tatttatata cttagacgtt tcaaacgtct taaaacgcaa attagagctt
      541 gataaagata tttgctcgtg tgccgacttt tttaaaagtc taggcacacg ccatgacaaa
      601 gctgaaataa actgcttcag ctttgtcatg gcggattcgc tcacttgaaa aagtgttcat
      661 ttcgctcgat tattagcata tattttttaa ctttttttgc tagccaaatt ttgcattagt
      721 tcgctcataa atcccaccct ttcagtacgt cctacggacg tatcgttcgt aatgtgaaag
      781 tacctttaaa ggtactttct acaaaactca ctaaagtgtt tggcaagctc tatatttgct
      841 agccaaatac ctacgtattt ggtgcaaata accgcttgtc aaaggggtgc aagctccccc
      901 ttgaatcccc ctcaaaaccc acgctccaca atacaaaaaa ggctagcaaa tgctagccac
      961 tttttgtaaa gtttcgcttg tttcaccttc ggtgaaatta ttgttttgta atatcaaaca
     1021 actattcatc aatcagcttt aaaaaattca attggtttag ctgtcccttc tgtcccatca
     1081 ttcgttgtca aaataaatac gagctttttt ggagaatcca aactaaaagt gtaatctaat
     1141 tgttttttat tagagcgcag tgttagtaaa ttatttgttg ctttgtaaat gaaaacttgt
     1201 tcatttatat ttaaattttt atcaatgatt tgaattttat gattgttctc ttttactaag
     1261 atggtatatt gttctatatt ttttgaagta tttaaattag tgattactag acgttctgaa
     1321 tgatctttag tttgccaagt tcctagaaaa ggaatcagat cagtcttttg tatttcttgt
     1381 ttttttgaac aactagttaa gaaaagaact aacactagac ccataactaa agcaatgggt
     1441 ttatttacca atttgtaatg gtattgtccc aagtaaaacc acctccaggt acaggaattg
     1501 taactggtcc tgcatttgca cttattacag ttgggtagtt ataccaagga ttccacacat
     1561 agtaagtttg ataaccacct tgattgaccc acccaaataa tgcaagtgca tgacggctgt
     1621 tactataatt tccataacca gcagttccca tataaatggc atttcctttt cttagttgtg
     1681 tttggacctc tgaaaggttt agtattcgtg ctactttttt aggataaaca ccacagtaat
     1741 ttgcatattt tattatttga tcttgattaa gactttttga ttcaatttga ctattccaat
     1801 catcaaggaa aagaggagac ctagataaat tttctttttg ggtttcaaaa taaccacgcc
     1861 tttgtgttaa atttaagtgg tatacaccta taattatata attaaaatat acaatatgcg
     1921 ataacaaatt tttgttatag ttcataaaat attgttttgg gaacataatc gttatttatc
     1981 gagctagtta acataatgtc gactatgcca agttgcccct ctaccaatgg atagagacgc
     2041 taactttgtg atttttaatt ggtctagcta gttactagct tctaatgctt gattttacgc
     2101 gatttctctt ttttagttct ttgtgcattt ttatctgtca ttttttaaag acttgttatt
     2161 tttgagagga tttgatatgc tttttttgtc tttctctagt tcttcacttt gtaatatttt
     2221 tatgttgatg aataggataa tctcattttg ggctgctcgt gagagcagtc tttttttgtt
     2281 tcagggtacg tcctattctt tggatttccg cgctattaaa taaccgatac ttggggattg
     2341 gggtagcgcc ccaaaataca aaaagaagaa gttgcataag cggatttttc ttttttttcg
     2401 caagttggta ccaacttgca aatcttgctg gaagactgat ccctaaaaag aaatcgagga
     2461 atttttttag ggatcggttt ctttttttat ctttttagaa agtttgttgg gtcaaaattt
     2521 ccagaagtaa aggtttgatt ggtttctttt tgacgatttt tgggttgatt tcgtcgggaa
     2581 ggattgagtt gattttcaat tttttctttc acttcttgat acactttaga atttgtaccg
     2641 ataagaacac cagtatcttt tagatataaa tcagcaaatt ctgccatgat ttctgtcatg
     2701 atagaaattt cttttcccat ggcattgagt tttgcttggt tactggttgt ggttgtattg
     2761 gtatcaggtt cataactcat acataaaaaa cgaatggctt ctgaataatt gttgacgtct
     2821 ggattttttt cgatgatgga atctaaaacg tcaacgtgac tgggataaag ggttacgtgt
     2881 ttttgaacag aagtttttct catgttatat tcctccgata agtgtttcaa tgagttggtt
     2941 gtttgtgtga acatagtcat tcagtatgtt cgtattttct gtttgaatgg caataaattt
     3001 ttcgagtaat aaatcgaatt gatctttttt gtaattcata agttgacggt caaaatcact
     3061 ttcgattaga acttttagat atttatttcg actccatttt ttgcccgttt tggttgtgag
     3121 ttcctgacaa cgtttatcta ttcttgcaat aattttggga ttgatatttc gaactaaaat
     3181 gtccatggaa attttccttt cgtatcagcg tataatttat gtataccata caaatatagt
     3241 atttgtatag ctatttttcg ccaaaacact atacatagcc tagccacaat ggcaaaaaag
     3301 tgatagcaaa tttttttctg agaaacgtga taggcacagc ctatctagca cctttcgtaa
     3361 gaaagtgata ccacgtttcc ttatgctctt tcaaaattca gaaaaatcag ctgtaaaacg
     3421 agtgcagtcc gagtaagatt caacgaaaaa acggggattg gggcgccacc aaaatatcgc
     3481 aacatgggtc catgttgctc tgctcgcaaa agcaaaaaga agaataaaac cagcaatttt
     3541 tattaattta aattgctggt tttattgcca gaattgccac cattttttct ccgtctttga
     3601 ttgtttttct atcgattctg tttcttcaga aagagtcgtt gatttatttt ccgaagattc
     3661 ttccgtataa gtcaactgta gttgttcctg cagtttctcg atttgttggt tggcttgcag
     3721 ggtgagttgt tgttggtggt cgagtaattt ttgcatttgt tttatttgct cgtctttttc
     3781 ttgtagttgc atatcttttt gatttaactg ttgttctagg agagaaagga cttctaattc
     3841 gggaacttgg ttggcgtttt tgtgggtttc ggttttcgtt ttttcgccaa ctagttgttg
     3901 atttgagttt tcgttttcgt taaaaaacat tgattttata gccttttgtc cggtttcatt
     3961 aatcacaaac ttgtttccga ttttcgaaaa ccaaagtttt cgattttcgt cagaaacttt
     4021 tttgttaatt gctgttttac taactcctaa ttcttcagca agttctttga ttgttttttc
     4081 tgtcataaaa tctaaaaacc cctcaatctt tgaataagtt ttgaagattg tctaataagt
     4141 ctttttttag ttctgaagga atatcggaat ttatctctga tttttgtgca ttattttctt
     4201 tattttgggt attttgttct ctttctaact tttctaactg ttgtaaaagt tccaattttc
     4261 gcttttgttc tttgattttt tcttgtaatg aagtaggtgc tttttcagat tgaacttgtt
     4321 ggttagctag ttctaatgct ttgttttgtt cttcttttgt tggggcatgt ttgttaaagt
     4381 cgtctgattt ttttatctca ggtttaaatg taaattgata gccaatgaca ggctttcccc
     4441 gtccttttcc gtatttcttt ttgattgtta aacctttaaa gattgcggtt agttcttgtc
     4501 gtattggatt gaacacacgt tgatcaatcg taccttggtt gtaactttta ggaatatcaa
     4561 gtaattcatg aaagtcttct tttgaaaaat aagcgaaacc tttggttctg tattgtttta
     4621 gtaatcgaaa cattgttttt gaataactgc tttctaattc attgaattgt tggagagaat
     4681 agcgcaccca ttcttcaaga ttattaagta agggtaaggc tttttcatga acttgtattt
     4741 cagcaaaagg aatatcagat tttccgtcga ttttaaattg attaaataaa acaaaacgtt
     4801 cacgttgcaa accgtcagca cttcttctac caaaacgtaa atccattaat ttgtcatacg
     4861 ttgtttctaa atcatctatg aatcgaacat ttgcagttgc tttataattg cttaaatctt
     4921 ttaattgctc gaatgtaaat tgtacttttt tatcacctac atcacgcatt cttgatacga
     4981 tagaaaagaa caaattcatt tcgactggtg taaattttcg caacggaatt gtatttaatt
     5041 catgatgata ctttacgatt tcattagaca tatttaaaat agctcctttc ttactcgcac
     5101 aagagataca cgttatgaaa tacaaaatgc ctgtttatct acatcttata ttaacatcgt
     5161 cgatgtacta attcaatgta caaacagaca aaacgatgta gataaacaga ca
//
