LOCUS       NZ_AP026572             1953 bp    DNA     circular CON 04-DEC-2023
DEFINITION  Enterococcus faecium strain JHP9 plasmid pJHP9_5, complete sequence.
ACCESSION   NZ_AP026572
VERSION     NZ_AP026572.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00466802
            Assembly: GCF_026073115.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1
  AUTHORS   Hashimoto,Y., Suzuki,M. and Tomita,H.
  TITLE     Analysis of enterococcal linear plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1953)
  AUTHORS   Hashimoto,Y. and Tomita,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2022) Contact:Yusuke Hashimoto Gunma University,
            Bacteriology Graduate School of Medicine; 3-39-22, Showa, Maebashi,
            Gunma 371-0804, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 2.1.1
            Genome Coverage                   :: 50x
            Sequencing Technology :: Illumina miniseq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/04/2023 06:09:23
            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)                     :: 3,420
            CDSs (total)                      :: 3,328
            Genes (coding)                    :: 2,997
            CDSs (with protein)               :: 2,997
            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)              :: 331
            CDSs (without protein)            :: 331
            Pseudo Genes (ambiguous residues) :: 0 of 331
            Pseudo Genes (frameshifted)       :: 142 of 331
            Pseudo Genes (incomplete)         :: 179 of 331
            Pseudo Genes (internal stop)      :: 86 of 331
            Pseudo Genes (multiple problems)  :: 68 of 331
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026572.1.
            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..1953
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="JHP9"
                     /isolation_source="sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pJHP9_5"
                     /geo_loc_name="Japan"
                     /collection_date="2000"
     gene            complement(765..1730)
                     /locus_tag="OQH78_RS17060"
                     /old_locus_tag="EfmJHP9_34340"
     CDS             complement(765..1730)
                     /locus_tag="OQH78_RS17060"
                     /old_locus_tag="EfmJHP9_34340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305972.1"
                     /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="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002304946.1"
                     /translation="MSKNGTIVNEWENLTALSNRRLNVKTFYTPLKIRWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRLNENNGYVKSVGLNGWQIVDKHDENIAYIEILKYQE
                     GQGRIDFNPNKINQFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDDFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKAVVPKEIETWWRLELQLRRG
                     KATDWHKMVHESLDSFASPHFLPIDTKHTDRIMIAGLMSDHSLWSGLTRPTKYKYRNLL
                     KQESQNDELTNHLRETFSESADNLKQELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(769..1648)
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.271"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ataacaccag aaaacaaaaa ctgacaaata ctcccgagta taaaagacac aagaccttgg
       61 ggaatgtcat tccccaaacc ccttgagcct cctcctgccg aaatggaagg gcgcacccgc
      121 tgtttatttc attcagctat cggctttcac aatctaacac gaccgttccg ctaccagtcg
      181 ccttacaggc tccattctcg ctcctctaac gtgttttaac gattgtgccg ataactaaac
      241 gaaataaacg ctaaaaccgc tcagaacgca aaatatgccg ttttagagct attgtagaaa
      301 atgtagtttg aaatgcaatt ttcttctttc agctttttat ttcccacttg taaatctgct
      361 aattattttc taccagacaa accattgatt ttttggctat cagttaactc acgattatta
      421 tgagaaatgc ttgtattctt tgttcccttt ttgaacgaaa tactgaaccc caagttaaaa
      481 ccctccttcg gctgtcgcta ataaaaagag tgtaaacctt tctgttactc tttgtcaaag
      541 agtaacattt tcctaattgt gacatggctg tcacaattcc aaacgctctc cgagggtttt
      601 cgctgtcaca agtgacaacg aaaaaaggag ccgaaagcgt gtcacgctct caactccttt
      661 tacgctttat tttgcttcat gcaaaatatt cgcttatcgt gaatttacgt cactaaacat
      721 tgacgcaaat ccactctcac tcatctgact tttcttattc ggtatcactt ctctgtcacg
      781 tccaacccca aaagccacgt gtctaattct tgtttcaaat tgtctgccga ttccgaaaat
      841 gtttctcgta aatgattcgt caattcatca ttctgactct cttgttttaa caaatttcga
      901 tatttgtatt tagttggtct agttaacccc gaccataaag aatggtctga cattaaacca
      961 gcaatcataa ttctatctgt atgttttgta tctattggta aaaagtgtgg actagcaaaa
     1021 ctatccaaac tttcatgaac cattttgtgc caatcagttg cttttcctcg gcgcaactgt
     1081 aattctaaac gccaccaagt ctcgatttct tttggcacga ctgctttttt tcgttcctgt
     1141 tccagctttt tattgtacat acgaacttga cgttcactag cacgactgcc ccaataagca
     1201 gtttctaact tgccagaccg accataaatt ggtttaaagg atacaggatc aaccacccga
     1261 tattgggtaa tgaaatcatc tggtacgtca attatatcgc aagcaatatc tgcacgtgaa
     1321 aaatgcggct ccaaaaataa atcatggata aaattcttca tcgagctagc taaaaactga
     1381 ttaattttat tcggattaaa gtcaattcgc ccttgccctt cttgatattt caaaatttca
     1441 atgtaagcaa tattctcatc atgcttatcc acaatttgcc aaccatttag accaacagat
     1501 ttaacataac cattattttc attcagtcgc attaactgtt caaagtctaa aatcaataca
     1561 tcattttgag tatgataata aatattttct ttcagttttc caacaatggt aattcggtca
     1621 attgaccacc gtattttcaa gggggtgtaa aaagttttta catttaaccg cctgttagat
     1681 agggctgtta aattttccca ctcatttaca atcgtgccat ttttactcaa atttcgttcc
     1741 tcctcaaaga aaaaagagat tcttggaaag aattttaaaa gttcacgtaa cccttaaaat
     1801 tcattaacaa gaatctctag tcttgaagaa acctaaaaat attcgtataa tgattatgag
     1861 ttacggagct agtgcgatag tttccgtaat tagtcgaaag gtgcttccaa caccaatcgg
     1921 ctattttttt gctctttttt cgatttttga taa
//
