LOCUS       NZ_AP024842             5849 bp    DNA     circular CON 04-NOV-2023
DEFINITION  Enterococcus faecium strain AA622 plasmid pAA622-5, complete
            sequence.
ACCESSION   NZ_AP024842
VERSION     NZ_AP024842.1
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  JOURNAL   Unpublished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 5849)
  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
            AP024842.1.
            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..5849
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="AA622"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pAA622-5"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            426..1403
                     /locus_tag="LDN47_RS16300"
                     /old_locus_tag="GVanDAA622_33400"
     CDS             426..1403
                     /locus_tag="LDN47_RS16300"
                     /old_locus_tag="GVanDAA622_33400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /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_002338009.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIAYFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEEQNKALELVNQQIYSEKDPTSLQEKIKEQKRKLELLQQLEE
                     LERKQNNLNKENKEINEQIPDNNSDIPPELKKGLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            1413..1910
                     /locus_tag="LDN47_RS16305"
                     /old_locus_tag="GVanDAA622_33410"
     CDS             1413..1910
                     /locus_tag="LDN47_RS16305"
                     /old_locus_tag="GVanDAA622_33410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /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_002347002.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNIIYLKKEA
                     VTTITKVLSGNEPGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQLALETQQK
                     LLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQSKTEKKWWQF
                     WQ"
                     /name="DUF536 domain-containing protein"
     gene            2286..2567
                     /locus_tag="LDN47_RS16310"
                     /old_locus_tag="GVanDAA622_33420"
     CDS             2286..2567
                     /locus_tag="LDN47_RS16310"
                     /old_locus_tag="GVanDAA622_33420"
                     /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_000353845.1"
                     /translation="MDILVRNINPKIITRIDKRCQELTTKTGKKWSRNQYLKILIENDF
                     DHELMNYKKDQFDLLFEKFIAIQAENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2569..2976
                     /locus_tag="LDN47_RS16315"
                     /old_locus_tag="GVanDAA622_33430"
     CDS             2569..2976
                     /locus_tag="LDN47_RS16315"
                     /old_locus_tag="GVanDAA622_33430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002364712.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223924344.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PATNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKLKI
                     NSILPDEINPKIVKKKPIKPLLLEILTQQTF"
                     /name="hypothetical protein"
     gene            3592..4746
                     /locus_tag="LDN47_RS16320"
                     /old_locus_tag="GVanDAA622_33440"
     CDS             3592..4746
                     /locus_tag="LDN47_RS16320"
                     /old_locus_tag="GVanDAA622_33440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348970.1"
                     /GO_function="GO:0008234 - cysteine-type peptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0006508 - proteolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="C47 family peptidase"
                     /protein_id="WP_002348708.1"
                     /translation="MIILKPKKKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPI
                     EEQAINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDA
                     DNTIKYIYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIK
                     LLWKSPLSTEKNGVSSFTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMI
                     NWRIAETQTSFPWCAAYVEAAILCNKTDVHATSARAIMHYTYPNLNNSQIESKSLNQDQ
                     IIKYANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQ
                     GGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="C47 family peptidase"
     gene            4719..5162
                     /locus_tag="LDN47_RS16325"
                     /old_locus_tag="GVanDAA622_33450"
     CDS             4719..5162
                     /locus_tag="LDN47_RS16325"
                     /old_locus_tag="GVanDAA622_33450"
                     /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            5419..>5609
                     /locus_tag="LDN47_RS16330"
                     /pseudo=""
     CDS             5419..>5609
                     /locus_tag="LDN47_RS16330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016628695.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     Typing          427..1403
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaactgtttt taagcaaagg agcctttagg cgactgcgca gtataatgtg agagcgtagc
       61 gatcacacat ttttagtgac cgtagggagc gagtttccca gtttagaaaa attcgcgaac
      121 ttgtttgagg aaaaaagcag gagtttttta ggcgggaaat tttgcctcct cttttataat
      181 ctctttttaa acctcttttt aaacctcttt accgtcggct gtatgcttac tctcccaagg
      241 tgtgcagaat cttttggggg tctttttgtc tgtttttagg ggtctttttg tctgttttta
      301 ggggtctttt tgtctgtttt tgggggtctt tttgtctgtt tttaggggtc tttaattagg
      361 ggcttgaccc ctattagaaa gctctttata attttgttaa gtagttaatc ttgaaggagg
      421 attttatggc aaatgaaatt gtgaaatacc accatgaatt aaatacgatt cctttacgca
      481 aatttacgtc agtagaaatg aatttattct tctctatagt atctagaatg cgtgacgtag
      541 gcgataaaaa agtacaattt acattcgaac aattaaaaga tttaagcaat tataaagcaa
      601 ctgcaaatgt tcgattcata gatgatttag aaacaacgta tgacaaatta atggatttac
      661 gttttggtag aagaagtgct gacggtttgc aacgtgaacg atttgtttta tttaatcaat
      721 ttaaaatcga tggaaaagct gatattcctt ttgctgaaat acaagtccat gagaaagcct
      781 tacccttact taataatctt gaagaatggg ttcgatattc tctccaacaa ttcaatgaat
      841 tagaaagcag ttattccaaa accatgttta gattattaaa acaatacaga accaaaggaa
      901 ttgcctattt ttcaaaagaa gactttcatg aattacttga tatccctaaa agttatagag
      961 aaagtgatat aaataaaaaa attataaagc ctattcgcca agaactaacc gcaatcttca
     1021 aaggtctgac aatcaaaaag aaatacggaa aaggaagagg aaaacctgtc attggctatc
     1081 aattcacgtt taaacctgaa ataaaaaaag cagacgactt taataaacac gcaccaacaa
     1141 aagaagaaca aaataaagct ttagaactag ttaatcaaca aatttactct gaaaaagacc
     1201 ccacttcatt acaagaaaaa atcaaagaac agaaacgaaa attagaactt ttacaacaat
     1261 tagaagagct agaaagaaaa caaaataatc tgaataaaga aaataaggag attaacgaac
     1321 aaataccaga taacaattcc gatattcccc cagaattaaa aaaaggctta ctagataatc
     1381 ttcaaaactt atttaaagaa taaggggttt ttatgacaga taaaactatc aaagaattag
     1441 cagatattct aggtgtttca aaagataaag tgaagtatca actgaggaaa ttacctagta
     1501 attttaccta caaaaaagga aatattatct acctgaaaaa agaagcagta acaacaatta
     1561 caaaggtttt atcaggtaat gagccgggta acttacctag tgaattacct gattcattac
     1621 ctaccgatta cctactcaag gagattgaaa ctaagaataa tcatattgaa gaaaaagata
     1681 ggcaaattga aaaacttcaa ctagctttag aaacacaaca aaaattactc gaccagcaac
     1741 aacaactcac cctgcaagcc aaccaacaaa tcgagaaact gcaggaacaa ctacagttga
     1801 cttatacgga agaatcttcg gaaaataaat caacgactct ttctgaagaa acagaatcga
     1861 tagaaaaaca atcaaagacg gagaaaaaat ggtggcaatt ctggcaataa aaccagcaat
     1921 ttaaattaat aaaaattgct ggttttattc ttctttttgc ttttgcgagc agagcaacat
     1981 gggcccatgt tgcgatattt tggtggcgcc ccaatccccg ttttttcgtt gaatcttact
     2041 cggactgcac tcgttttaca gctgattttt ctgaattttg aaagagcata aggaaacgtg
     2101 gtatcacttt cttacgaaag gtgctagata agctgtgcct atcacgtttc tcagaaaaaa
     2161 atttgctatc acttttttgc cattgtggct aggctatgta tagtgttttg gcgaaaaata
     2221 gctatacaaa tactatattt gtatgatata cataaattat atactgatac gaaaggaaaa
     2281 tttccatgga cattttagtt cgaaatatca atcccaaaat tattacaaga atagataaac
     2341 gttgtcagga actaacaacc aaaacgggca aaaaatggag tcgaaatcaa tacctaaaaa
     2401 ttttaatcga aaacgatttt gaccacgaac ttatgaatta caaaaaagat caattcgatt
     2461 tattattcga aaaatttatt gccattcaag cagaaaatac gaacatacta aatgactatg
     2521 ttcacacaaa caaccaactc attgaaacac ttatcggagg aatataacat gagaaaaact
     2581 tctgttcaaa aacacgtaac cctttatccc agtcacgttg acgttttaga ttccatcatc
     2641 gaaaaaaatc cagacgtcaa caattattca gaagccattc gctttttatg tatgagttat
     2701 gaacctgcta ccaatacaac cacaaccagt aaccaagcaa aactcaatgc catgggaaaa
     2761 gaaatttcta tcatgacaga aatcatggca gaatttgctg atttatatct aaaagatact
     2821 ggtgttctta tcggtacaaa ttctaaagta tatcaagaag tgaaagaaaa attgaaaatc
     2881 aactcaatcc ttcccgacga aatcaaccca aaaatcgtca aaaagaaacc aatcaaacct
     2941 ttacttctgg aaattttgac ccaacaaact ttctaaaaag ataaaaaaag aaaccgaaaa
     3001 ataaaaaaat tcctcgattt ctttttaggg atcggtcttc cagcaagatt tgcaagttgg
     3061 taccaacttg cgaaaaaaaa aagaaaaatc cgcttctgcg aattcttctt ttttcatttt
     3121 ggggcgctgc cctaatccct aagtcccggt tattcaatag catggaaact caaagaataa
     3181 gacgttccct ggaataaaaa aaaggctgct cgttcgagca gtccatacat aggaaaatga
     3241 aaaaacgacg tcccttactg agaaacgcta ttaaactttt aacaaatcct ctaaaaaata
     3301 acaagtcttt aaaaagtgac cggtaaaaat gcacaaagaa ctaaaaaaga gaaattgcat
     3361 caaatcaagc attagaagct agtaactagc tagaccaatt gaaaatcaca aagtgagcgc
     3421 ctgtatctat tgctacaggc gctacttggc atagtcgaca ttatgttaac taacgctata
     3481 aataacgatt atgttcccaa aacaatattt tatgaactat aacaaaaatt tgttatcgca
     3541 tattgtatat tttaattata ggtgtatacc acttaaattt aacacaaagg cgtgattatt
     3601 ttgaaaccca aaaagaaaat ttatctaggt ctcctctttt ccttgatgat tggaattttt
     3661 agtataggaa ttacaaatac ctatgcttca gaaaattcta atttcaatat caactcccaa
     3721 ccaattgaag aacaagcaat taattttgcg aaaactgatt ttgaacactc cataacttca
     3781 attcttttaa tggaaaataa caccgaaact gatattaact atactcttgg ttcgccattt
     3841 aaaatgctcg atggagaaaa tacggcaaat agttctattt tctttccagt attttcagac
     3901 gctgataata cgattaaata tatttatacc gtcaaaaaaa atacaaatgg agaatattca
     3961 ggaagtattt cacaattttt agcaaaagaa cttcaaaatc tagtagatag taatataaca
     4021 gatacaacct tattttttca agataatagc atttattatt ccgataatgg acaaattaaa
     4081 ctactttgga aatcaccttt aagtacagaa aaaaatggtg tttcttcctt tacagaaaaa
     4141 aatgatctta tatccgtaaa tataaaaaat aaaattaaaa atttctctaa aaaacaaaat
     4201 tttcctgcgg ttaaacgtgt aaaaagtgtc tcctccggag ataactttat tatgattaat
     4261 tggcgtatag cagaaaccca aacaagtttt ccgtggtgtg ctgcttacgt agaagctgct
     4321 atcttatgta acaaaacaga tgtacatgct acttcagcta gagccattat gcattatacc
     4381 tatcctaatt taaacaacag tcaaattgaa tcaaaaagtc ttaatcaaga tcaaataata
     4441 aaatatgcaa attactgtgg tgtttatcct aaaaaagtag cacgaatact aaacctttca
     4501 gaggtccaaa cacaactaag aaaaggaaat gccatttata tgggaactgc tggttatgga
     4561 aattatagta acagccgtca tgcacttgca ttatttgggt gggtcaatca aggtggttat
     4621 caaacttact atgtgtggaa tccttggtat aactacccaa ctgtaataag tgcaaatgca
     4681 ggaccagtta caattcctgt acctggaggt ggttttactt gggacaatac cattacaaat
     4741 tggtaaataa acccattgct ttagttatgg gtctagtgtt agttcttttc ttaactagtt
     4801 gttcaaaaaa acaagaaata caaaagactg atctgattcc ttttctagga acttggcaaa
     4861 ctaaagatca ttcagaacgt ctagtaatca ctaatttaaa tacttcaaaa aatatagaac
     4921 aatataccat cttagtaaaa gagaacaatc ataaaattca aatcattgat aaaaatttaa
     4981 atataaatga acaagttttc atttacaaag caacaaataa tttactaaca ctgcgctcta
     5041 ataaaaaaca attagattac acttttagtt tggattctcc aaaaaagctc gtatttattt
     5101 tgacaacgaa tgatgggaca gaagggacag ctaaaccaat tgaatttttt aaagctgatt
     5161 gatgaatagt tgtttgatat tacaaaacaa taatttcacc gaaggtgaaa caagcgaaac
     5221 tttacaaaaa gtggctagca tttgctagcc ttttttgtat tgtggagcgt gggttttgag
     5281 ggggattcaa gggggagctt gcgccccttt gaaaagcggt tatttgcacc aaatacgtag
     5341 gtatttggct agcaaatata gagcttgcca agcccttttg gtgagcttta ctcattgtgc
     5401 ctttttaggt acaatggtat tgcgaacgat acgtccgtag gacgtactga aagggtggga
     5461 cttatgagcg aacaaaatca aaatttggct agcgatcatt ctaaaaaata tacctatcga
     5521 tccaagccaa aacaaatcag ttttcgagtg agcgaatctg aatttgcaaa gcttcagctt
     5581 tgcaaatgag tgtgccggct tccgtaaaaa tacatatggc tataatttgc gttttaaggc
     5641 gttttaaacg ttctggtata taatttatac caaaacaact ttaaaacgcc ttagatctaa
     5701 ttttagaggt cttatagaac attttagggt tgttagggct tgccctgacc gcctgtaagg
     5761 cgctttgaga acaagataag ggttttatac taagactgtc ttaaaacggc ttaaacaaac
     5821 gctcagaact tttcaaagga gttctttat
//
