LOCUS       NZ_AP024843             4373 bp    DNA     circular CON 04-NOV-2023
DEFINITION  Enterococcus faecium strain AA622 plasmid pAA622-6, complete
            sequence.
ACCESSION   NZ_AP024843
VERSION     NZ_AP024843.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00324536
            Sequence Read Archive: DRR305792
            Assembly: GCF_019977575.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1
  AUTHORS   Hashimoto,Y. and Tomita,H.
  TITLE     olecular characterization of the VanD-type vancomycin resistant
            Enterococcus faecium clinical isolates from a patient after
            vancomycin therapy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4373)
  AUTHORS   Hashimoto,Y. and Tomita,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2021) Contact:Yusuke Hashimoto Gunma University
            Graduate School of Medicine, Bacteriology; showa 3-39-22, Maebashi,
            Gunma 371-0034, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: canu v. 2.1.1
            Genome Coverage                   :: 80x
            Sequencing Technology             :: Illumina Miseq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/04/2023 02:43:55
            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)                     :: 3,289
            CDSs (total)                      :: 3,198
            Genes (coding)                    :: 2,960
            CDSs (with protein)               :: 2,960
            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)              :: 238
            CDSs (without protein)            :: 238
            Pseudo Genes (ambiguous residues) :: 0 of 238
            Pseudo Genes (frameshifted)       :: 156 of 238
            Pseudo Genes (incomplete)         :: 82 of 238
            Pseudo Genes (internal stop)      :: 44 of 238
            Pseudo Genes (multiple problems)  :: 37 of 238
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024843.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..4373
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="AA622"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pAA622-6"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            join(4367..4373,1..946)
                     /locus_tag="LDN47_RS16335"
                     /pseudo=""
     CDS             join(4367..4373,1..946)
                     /locus_tag="LDN47_RS16335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /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="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            949..1182
                     /locus_tag="LDN47_RS16340"
                     /old_locus_tag="GVanDAA622_33470"
     CDS             949..1182
                     /locus_tag="LDN47_RS16340"
                     /old_locus_tag="GVanDAA622_33470"
                     /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            1175..1594
                     /locus_tag="LDN47_RS16345"
                     /old_locus_tag="GVanDAA622_33480"
     CDS             1175..1594
                     /locus_tag="LDN47_RS16345"
                     /old_locus_tag="GVanDAA622_33480"
                     /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            1603..1911
                     /locus_tag="LDN47_RS16350"
                     /old_locus_tag="GVanDAA622_33490"
     CDS             1603..1911
                     /locus_tag="LDN47_RS16350"
                     /old_locus_tag="GVanDAA622_33490"
                     /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_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            1915..2277
                     /locus_tag="LDN47_RS16355"
                     /old_locus_tag="GVanDAA622_33500"
     CDS             1915..2277
                     /locus_tag="LDN47_RS16355"
                     /old_locus_tag="GVanDAA622_33500"
                     /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_223924346.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     gene            2499..3905
                     /locus_tag="LDN47_RS16360"
                     /old_locus_tag="GVanDAA622_33510"
     CDS             2499..3905
                     /locus_tag="LDN47_RS16360"
                     /old_locus_tag="GVanDAA622_33510"
                     /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_217277483.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDIGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          63..936
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2500..3902
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaatgagtg ggaaaattta acagccctat ctaacaggcg gttaaatgta caaaatatgt
       61 acaccccctt aaaaatgcag tggtcaattg accgaattac tatcgttgga aaactgaagg
      121 aaaatattta ttatcacact caaaatgatg tgttgatttt agattttgag caattaatgc
      181 gggtgaatga aggcaatggc tatttaaaag cggttgggaa taacggctgg caattattag
      241 accaatacga agaaaatatt gcttatattg agattttgaa atggcaagat ggcaaagggc
      301 ggattgattt taacccgaat aagattggtc atttttagct agttcaatga aaaatttcat
      361 tcatgattta tttctagaac cacatttctc acgtgcggat attgcttgcg atattatcga
      421 tgtgcctgat gagtttatta cacaatatcg agtggttgat cctgtttctt tcaagccaat
      481 ttatgggcgg tctgggaagc tggaaacagc ttattggggc agtcgtgcca gcgaacgcca
      541 gattcggcta tacaacaaaa aattggaaca ggaaaccaag cgtaaaattg tgccaccaga
      601 aatagaaact tggtggcgac tggaattgca gttaaggcgt gggaaagcaa cagattggca
      661 tgcaatggtt catgaaagtt taaatagttt tgctagccct cattttctac cacttgatgt
      721 aaaaacaaat gataaggtga tgatttttgg actgattgct aaccctgaaa tgtgggggtt
      781 tttagagcgt agaatgaaat acaaattgag agatattttg aaaagagaaa gtcaaaatga
      841 tgagttgacg aatcatttac gagaaacatt ttcggaatca gcagatgttt tgaaaaaaga
      901 attagacact tggcttcaag ggttagatgt aacggaggag gaataagaat ggcagaaaaa
      961 caaaagcatt ttggtaagaa aaattggttg gtgaatttaa caggtgataa cgttgtcgtt
     1021 gtttttttgg atagcaaaaa aatgtccggt aagttacttg atgtaacgca gtatgagttg
     1081 attttgaaaa ataataaaat tgattcccca atcattatcc ctaagcatgc tgttaaatat
     1141 gtttatgggg tagctgaaag taacggagaa gataatgact gatttgccag aaaaaatgac
     1201 cataaaaaac cttgctgatg agttgggtat atctaaaaat acagtgcgca atcaactggt
     1261 caatgcaggt tatgaccttg ctcggtataa agataatggg gttatcatgt tagacaagga
     1321 attgattggt gttgtgcggt caatttatcg gtcaaaaggt ggtcaattga ctggtgattt
     1381 accggtcaat gatgcaggca atgatttccc gttagaaaaa gaaaatgaat ttttgcgtga
     1441 acaattagcg gaaaaagata ggcatatttc tgaattaacg gaaatgattc gtgaccaaca
     1501 aaaattgact ttgcttcagc aacaaaaaaa cgatcagttg ttactagaaa atcaagaatt
     1561 aaaaaatcga aaatggtggc aattctggaa gtgaggtgtg acatggataa aattgatttg
     1621 agagaagaaa cagtcgatag aattgaattg atgtatgaac ggttagctga ttatttgaat
     1681 ttgccggatg aagataatta tagtgaaatg cttgaacgaa tgatggatgt tctcaactcg
     1741 gttatcaatg ctgatctagc aaaatcttca gttttgacta atgaatttgt tcataagcat
     1801 ttagcgcaaa caactgatga atcagaaaaa gaattttggt tgaaattaat gagtcatgtt
     1861 atgcagttaa accaaatttc cgttattaat tccaaagaaa aggagatgta gtttatggga
     1921 atgactttag cagatattaa agcgcaagaa gaaaaattaa aaaaagaaca agcgaaactt
     1981 cgccaacaga aaaaacgctt gattgagaaa gaaaatgctg caatgggcaa ggctcttcgc
     2041 aagcgttttg ggtttgaaac ttttgctgat tttgagcggt ggctatcgtc gatttctgac
     2101 gatcagcaac acgaaaaatc agtggataat gagtggcttg ctgatgaaaa atcagcgcca
     2161 agcgaacgag attatcccga tgaatctgac ggcttattcg gagtgatacc gaataagaaa
     2221 agtcagatga gtgagagtaa atttacgtca atgtttaatg acgtgagttt acgataagcg
     2281 attattttgc gtgaagcaaa ataaagcgta aaaggagttg agagcgtgac acgctttcgg
     2341 ctcctttttt cgttgtcact tgtgacagcg aataccctcg gagagcattt ggaattgtga
     2401 cagccatgtc acaattagga aaatgttact ctttgacaaa gagtaacaga aaggtttaca
     2461 ctctttttat tagcgacagc gcgaaggagg gttttaactt ggggtttagt atttcattta
     2521 aaaaaggaac gaagaataca agtatttctc ataataatcg tgagttaact gatcgccaga
     2581 aaaccaatga ttggcataag catattgact tcacgaaatc ggatgaaaat atttatttag
     2641 agcagacgaa tctagcagat aaatatgagg aattgtttgg cgaagtggta gaaaaatata
     2701 atgcgaaaca aaaaagagcc gatagaaaaa tcgaggacta tttagcgaaa gtgcgcaagg
     2761 ataaaaagtt ggaacctcaa cgagaattta ttgtgcaaat aggcatttta gatgatttcc
     2821 agacaaatcg agcagatggt tcttctactg gcatatcgaa acaacaagct gaacaaaatc
     2881 gagtgattgc caataaaatt ttggttcagt attacaagga gtttcaagag agaaacccta
     2941 atttggctgt ttataatgct gttattcata atgacgaaat aagtccgcac ctgcacttga
     3001 atattgtgcc ggttgctgaa ggttataaac ggggtgttca aaagcagccg agctttaata
     3061 aagcactggt tcaacaaggg atacacgctg ataaagataa tggtcgagtg cttttcaata
     3121 attttagaaa tcaagaagtt gactctatag aacgattaat gaatgattac ggttggaaaa
     3181 gggatattgt cggtaccaac aaaattaaag atattcacga atacaaagaa atcatgagtg
     3241 aaatttctga attgcgccaa acggctgtaa aagagcgtga gagcgtttct gatgagttga
     3301 ggtatattta taggcaaaga gaagaaaacg agcgtgataa ggctctgatg gcttctgaga
     3361 gagcgaagat tgaagaagag aagaaaaata tgctgaatgt aaaaaaagag atggcggtca
     3421 ttttccaaaa agatatggtt cctttagaaa gtttcaagag gcttcctgat ggttcgtatc
     3481 atttatctgg gaatgatttt gttgatttgt atcaacgagc tacgagagca acaaatgcca
     3541 agagaaatgc tgataacatg agtgagcaat atttacagat gcttgagcaa aatacagaat
     3601 taaatgagta tgtagctaca ttggaagaag agcgtcattt gtctggtaga aaacaattag
     3661 cagatttaca agtggaaaat aaaaagctga aagaagaaaa tcgctcttta cgccagcgtt
     3721 tagagcgatt aaaaaacgca tttcaaaaat cgatcactcg tttgtctatc cgttttggtc
     3781 ttgcagaaaa ggatataggg ctttctgagg aattagaagt gttagagcag gagaaaacct
     3841 tattttatcg tcaaaacgtc tcacagcgta aattagagcg ttctgaagat gagatcgagt
     3901 ggtagttacg atgtgcagtc aacggtaccg gaggcggttt gtgccgagga taaggagttg
     3961 acggctaaac cactagccta ttaagctgac atttgctaaa aaatggccag tccatttttt
     4021 ggccaaccta gcgttagcga agtttggggg cgcccttttc aaagggtgcg gttttatttt
     4081 ttggatattt gcatagctaa agagaagtgc tattattgag ttagcaaaca aatgaactga
     4141 aaaaagagta aaaaaatagt cgagcaacgc taccaacgtt ctcgaccttt acggaaacta
     4201 atcgcactag ctccgtaact tcttaatcat tatacgaata tttttagatt tcttcaagac
     4261 tagagatttt ttggtaatga atttttaaga gttacgtgaa cttttgaaaa ttctttccag
     4321 aagtctcttt tttctttgag gaggaacaaa atttgagtaa aatggcataa tcg
//
