LOCUS       NZ_AP026571             4378 bp    DNA     circular CON 04-DEC-2023
DEFINITION  Enterococcus faecium strain JHP9 plasmid pJHP9_4, complete sequence.
ACCESSION   NZ_AP026571
VERSION     NZ_AP026571.1
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  JOURNAL   Unpublished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 4378)
  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
            AP026571.1.
            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..4378
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="JHP9"
                     /isolation_source="sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pJHP9_4"
                     /geo_loc_name="Japan"
                     /collection_date="2000"
     gene            complement(join(4309..4378,1..242))
                     /locus_tag="OQH78_RS17030"
                     /pseudo=""
     CDS             complement(join(4309..4378,1..242))
                     /locus_tag="OQH78_RS17030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(251..670)
                     /locus_tag="OQH78_RS17035"
                     /old_locus_tag="EfmJHP9_34290"
     CDS             complement(251..670)
                     /locus_tag="OQH78_RS17035"
                     /old_locus_tag="EfmJHP9_34290"
                     /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            complement(663..896)
                     /locus_tag="OQH78_RS17040"
                     /old_locus_tag="EfmJHP9_34300"
     CDS             complement(663..896)
                     /locus_tag="OQH78_RS17040"
                     /old_locus_tag="EfmJHP9_34300"
                     /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            complement(899..1867)
                     /locus_tag="OQH78_RS17045"
                     /old_locus_tag="EfmJHP9_34310"
     CDS             complement(899..1867)
                     /locus_tag="OQH78_RS17045"
                     /old_locus_tag="EfmJHP9_34310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(2314..3720)
                     /locus_tag="OQH78_RS17050"
                     /old_locus_tag="EfmJHP9_34320"
     CDS             complement(2314..3720)
                     /locus_tag="OQH78_RS17050"
                     /old_locus_tag="EfmJHP9_34320"
                     /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_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(3942..4305)
                     /locus_tag="OQH78_RS17055"
                     /old_locus_tag="EfmJHP9_34330"
                     /pseudo=""
     CDS             complement(3942..4305)
                     /locus_tag="OQH78_RS17055"
                     /old_locus_tag="EfmJHP9_34330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(907..1784)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2318..3720)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcaaccaaa attctttttc tgattcatca gttgtttgcg ctaaatgctt atgaacaaat
       61 tcattagtca aaactgaaga ttttgctaga tcagcattga taaccgagtt gagaacatcc
      121 atcattcgtt caagcatttc actataatta tcttcatccg gcaaattcaa ataatcagct
      181 aaccgttcat acatcaattc aattctatcg actgtttctt ctctcaaatc aattttatcc
      241 atgtcacacc tcacttccag aattgccacc attttcgatt ttttaattct tgattttcta
      301 gtaacaactg atcgtttttt tgttgctgaa gcaaagtcaa tttttgttgg tcacgaatca
      361 tttccgttaa ttcagaaata tgcctatctt tttccgctaa ttgttcacgc aaaaattcat
      421 tttctttttc taacgggaaa tcattgcctg catcattgac cggtaaatca ccagtcaatt
      481 gaccaccttt tgaccgataa attgaccgca caacaccaat caattccttg tctaacatga
      541 taaccccatt atctttatac cgagcaaggt cataacctgc attgaccagt tgattgcgca
      601 ctgtattttt agatataccc aactcatcag caaggttttt tatggtcatt ttttctggca
      661 aatcagtcat tatcttctcc gttactttca gctaccccat aaacatattt aacagcatgc
      721 ttagggataa tgattgggga atcaatttta ttatttttca aaatcaactc atactgcgtt
      781 acatcaagta acttaccgga catttttttg ctatccaaaa aaacaacgac aacgttatca
      841 cctgttaaat tcaccaacca atttttctta ccaaaatgct tttgtttttc tgccattctt
      901 attcctcctc cgttacatct aacccttgaa gccaagtgtc taattctttt ttcaaaacat
      961 ctgctgattc cgaaaatgtt tctcgtaaat gattcgtcaa ctcatcattt tgactttctc
     1021 ttttcaaaat atctctcaat ttgtatttca ttctacgctc taaaaacccc cacatttcag
     1081 ggttagcaat cagtccaaaa atcatcacct tatcatttgt ttttacatca agtggtagaa
     1141 aatgagggct agcaaaacta tttaaacttt catgaaccat tgcatgccaa tctgttgctt
     1201 tcccacgcct taactgcaat tccagtcgcc accaagtttc tatttctggt ggcacaattt
     1261 tacgcttggt ttcctgttcc aattttttgt tgtatagccg aatctggcgt tcgctggcac
     1321 gactgcccca ataagctgtt tccagcttcc cagaccgccc ataaattggc ttgaaagaaa
     1381 caggatcaac cactcgatat tgtgtaataa actcatcagg cacatcgata atatcgcaag
     1441 caatatccgc acgtgagaaa tgtggttcta gaaataaatc atgaatgaaa tttttcattg
     1501 aactagctaa aaaatgacca atcttattcg ggttaaaatc aatccgccct ttgccatctt
     1561 gccatttcaa aatctcaata taagcaatat tttcttcgta ttggtctaat aattgccagc
     1621 cgttattccc aaccgctttt aaatagccat tgccttcatt cacccgcatt aattgctcaa
     1681 aatctaaaat caacacatca ttttgagtgt gataataaat attttccttc agttttccaa
     1741 cgatagtaat tcggtcaatt gaccactgca tttttaaggg ggtgtacata ttttgtacat
     1801 ttaaccgcct gttagatagg gctgttaaat tttcccactc atttacgatt atgccatttt
     1861 tactcaaatt ttgttcctcc tcaaagaaaa agagacttct ggaaagaatt ttcaaaagtt
     1921 cacgtaactc ttaaaaattc attaccaaaa aatctctagt cttgaagaaa tctaaaaata
     1981 ttcgtataat gattaagaag ttacggagct agtgcgatta gtttccgtaa aggtcgagaa
     2041 cgttggtagc gttgctcgac tattttttta ctcttttttc agttcatttg tttgctaact
     2101 caataatagc acttctcttt agctatgcaa atatccaaaa aataaaaccg caccctttga
     2161 aaagggcgcc cccaaacttc gctaacgcta ggttggccaa aaaatggact ggccattttt
     2221 tagcaaatgt cagcttaata ggctagtggt ttagccgtca actccttatc ctcggcacaa
     2281 accgcctccg gtaccgttga ctgcacatcg taactaccac tcgatctcat cttcagaacg
     2341 ctctaattta cgctgtgaga cgttttgacg ataaaataag gttttctcct gctctaacac
     2401 ttctaattcc tcagaaagcc ccatatcctt ttctgcaaga ccaaaacgga tagacaaacg
     2461 agtgatcgat ttttgaaatg cgttttttaa tcgctctaaa cgctggcgta aagagcgatt
     2521 ttcttctttc agctttttat tttccacttg taaatctgct aattgttttc taccagacaa
     2581 atgacgctct tcttccaatg tagctacata ctcatttaat tctgtatttt gctcaagcat
     2641 ctgtaaatat tgctcactca tgttatcagc atttctcttg gcatttgttg ctctcgtagc
     2701 tcgttgatac aaatcaacaa aatcattccc agataaatga tacgaaccat caggaagcct
     2761 cttgaaactt tctaaaggaa ccatatcttt ttggaaaatg accgccatct ctttttttac
     2821 attcagcata tttttcttct cttcttcaat cttcgctctc tcagaagcca tcagagcctt
     2881 atcacgctcg ttttcttctc tttgcctaga aatatacctc aactcatcag aaacgctctc
     2941 acgctctttt acagccgttt ggcgcaattc agaaatttca ctcatgattt ctttgtattc
     3001 gtgaatatct ttaattttgt tggtaccgac aatatccctt ttccaaccgt aatcattcat
     3061 taatcgttct atagagtcaa cttcttgatt tctaaaatta ttgaaaagca ctcgaccatt
     3121 atctttatca gcgtgtatcc cttgttgaac cagtgcttta ttaaagctcg gctgcttttg
     3181 aacaccccgt ttataacctt cagcaaccgg cacaatattc aagtgcaggt gcggacttat
     3241 ttcgtcatta tgaataacag cattataaac agccaaatta gggtttctct cttgaaactc
     3301 cttgtaatac tgaaccaaaa ttttattggc aatcactcga ttttgttcag cttgttgttt
     3361 cgatatgcca gtagaagaac catctgctcg atttgtctgg aaatcatcta aaatgcctat
     3421 ttgcacaata aattctcgtt gaggttccaa ctttttatcc ttgcgcactt tcgctaaata
     3481 gtcctcgatt tttctatcgg ctcttttttg tttcgcatta tatttttcta ccacttcgcc
     3541 aaacaattcc tcatatttat ctgctagatt cgtctgctct aaataaatat tttcatccga
     3601 tttcgtgaag tcaatatgct tatgccaatc attggttttc tggcgatcag ttaactcacg
     3661 attattatga gaaatacttg tattcttcgt tcctttttta aatgaaatac taaaccccaa
     3721 gttaaaaccc tccttcgcgc tgtcgctaat aaaaagattg taaacctttc tgttactctt
     3781 tgtcaaagag taacattttc ctaattgtga catggctgtc acaattccaa atgctctccg
     3841 agggtattcg ctgtcacaag tgacaacgaa aaaaggagcc gaaagcgtgt cacgctctca
     3901 actcctttta cgctttattt tgcttcacgc aaaataatcg cttatcgtaa attcacgtca
     3961 ttaaatattg acgtaaattt actctcactc atctgacttt tcttattcgg tatcactccg
     4021 aataagccgt cagattcatc gggataatct cgttcgcttg gcgctgattt ttcatcagca
     4081 agccactcat tatccactga tttttcgtgt tgctgatcgt cagaaatcga cgatagccac
     4141 cgctcaaaat cagcaaaagt ttcaaaccca aaacgcttgc gaagagcctt gcccattgca
     4201 gcattttctt tctcaatcaa agcgtgtttt ctgttggcga agtttcgctt gttctttttt
     4261 taatttttct tcttgcgctt taatatctgc taaagtcatt cccataaact acatctcctt
     4321 ttctttggaa ttaataacgg aaatttggtt taactgcata acatgactca ttaatttt
//
