LOCUS       NZ_AP024836             5850 bp    DNA     circular CON 04-NOV-2023
DEFINITION  Enterococcus faecium strain AA620 plasmid pAA620-5, complete
            sequence.
ACCESSION   NZ_AP024836
VERSION     NZ_AP024836.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00324535
            Sequence Read Archive: DRR305791
            Assembly: GCF_019977495.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1
  AUTHORS   Hashimoto,Y. and Tomita,H.
  TITLE     Molecular characterization of the VanD-type vancomycin resistant
            Enterococcus faecium clinical isolates from a patient after
            vancomycin therapy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5850)
  AUTHORS   Hashimoto,Y. and Tomita,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2021) Contact:Yusuke Hashimoto Gunma University
            Graduate School of Medicine, Bacteriology; 3-39-22, Maebashi, Gunma
            371-0034, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: canu v. 2.1.1
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina Miseq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/04/2023 02:38:58
            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)                     :: 3,169
            CDSs (total)                      :: 3,078
            Genes (coding)                    :: 2,876
            CDSs (with protein)               :: 2,876
            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)              :: 202
            CDSs (without protein)            :: 202
            Pseudo Genes (ambiguous residues) :: 0 of 202
            Pseudo Genes (frameshifted)       :: 135 of 202
            Pseudo Genes (incomplete)         :: 63 of 202
            Pseudo Genes (internal stop)      :: 48 of 202
            Pseudo Genes (multiple problems)  :: 37 of 202
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024836.1.
            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..5850
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="AA620"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pAA620-5"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
     gene            complement(531..947)
                     /locus_tag="LDN34_RS15745"
                     /old_locus_tag="GVanDAA620_31940"
     CDS             complement(531..947)
                     /locus_tag="LDN34_RS15745"
                     /old_locus_tag="GVanDAA620_31940"
                     /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_001232860.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PATNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(949..1230)
                     /locus_tag="LDN34_RS15750"
                     /old_locus_tag="GVanDAA620_31950"
     CDS             complement(949..1230)
                     /locus_tag="LDN34_RS15750"
                     /old_locus_tag="GVanDAA620_31950"
                     /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            complement(1606..2103)
                     /locus_tag="LDN34_RS15755"
                     /old_locus_tag="GVanDAA620_31960"
     CDS             complement(1606..2103)
                     /locus_tag="LDN34_RS15755"
                     /old_locus_tag="GVanDAA620_31960"
                     /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            complement(2113..3090)
                     /locus_tag="LDN34_RS15760"
                     /old_locus_tag="GVanDAA620_31970"
     CDS             complement(2113..3090)
                     /locus_tag="LDN34_RS15760"
                     /old_locus_tag="GVanDAA620_31970"
                     /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            complement(<3756..3946)
                     /locus_tag="LDN34_RS15765"
                     /pseudo=""
     CDS             complement(<3756..3946)
                     /locus_tag="LDN34_RS15765"
                     /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"
     gene            complement(4203..4646)
                     /locus_tag="LDN34_RS15770"
                     /old_locus_tag="GVanDAA620_31980"
     CDS             complement(4203..4646)
                     /locus_tag="LDN34_RS15770"
                     /old_locus_tag="GVanDAA620_31980"
                     /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(4619..5719)
                     /locus_tag="LDN34_RS15775"
                     /old_locus_tag="GVanDAA620_31990"
     CDS             complement(4619..5719)
                     /locus_tag="LDN34_RS15775"
                     /old_locus_tag="GVanDAA620_31990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010729425.1"
                     /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_222717721.1"
                     /translation="MIGIFSIGITNTYASENSNFNINSQPIEEQAINFAKTDFEHSITS
                     ILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDADNTIKYIYTVKKNTNGEY
                     SGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIKLLWKSPLSTEKNGVSSFT
                     EKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMINWRIAETQTSFPWCAAYV
                     EAAILCNKTDVHATSARAIMHYTYPNLNNSQIESKSLNQDQIIKYANYCGVYPKKVARI
                     LNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQGGYQTYYVWNPWYNYPTV
                     ISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="C47 family peptidase"
     Typing          complement(2114..3090)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cataaaatat tgttttggga acataatcgt tatttatagc gttagttaac ataatgtcga
       61 ctatgccaag tagcgcctgt agcaatagat acaggcgctc actttgtgat tttcaattgg
      121 tctagctagt tactagcttc taatgcttga tttgatgcaa tttctctttt ttagttcttt
      181 gtgcattttt accggtcact ttttaaagac ttgttatttt ttagaggatt tgttaaaagt
      241 ttaatagcgt ttctcagtaa gggacgtcgt tttttcattt tcctatgtat ggactgctcg
      301 aacgagcagc ctttttttta ttccagggaa cgtcttattc tttgagtttc catgctattg
      361 aataaccggg acttagggat tagggcagcg ccccaaaatg aaaaaagaag aattcgcaga
      421 agcggatttt tctttttttt ttcgcaagtt ggtaccaact tgcaaatctt gctggaagac
      481 cgatccctaa aaagaaatcg aggaattttt ttatttttcg gtttcttttt ttatcttttt
      541 agaaagtttg ttgggtcaaa atttccagaa gtaaaggttt gattggtttc tttttgacga
      601 tttttgggtt gatttcgtcg ggaaggattg agttgatttt caattttttc tttcacttct
      661 tgatatactt tagaatttgt accgataaga acaccagtat cttttagata taaatcagca
      721 aattctgcca tgatttctgt catgatagaa atttcttttc ccatggcatt gagttttgct
      781 tggttactgg ttgtggttgt attggtagca ggttcataac tcatacataa aaagcgaatg
      841 gcttctgaat aattgttgac gtctggattt ttttcgatga tggaatctaa aacgtcaacg
      901 tgactgggat aaagggttac gtgtttttga acagaagttt ttctcatgtt atattcctcc
      961 gataagtgtt tcaatgagtt ggttgtttgt gtgaacatag tcatttagta tgttcgtatt
     1021 ttctgcttga atggcaataa atttttcgaa taataaatcg aattgatctt ttttgtaatt
     1081 cataagttcg tggtcaaaat cgttttcgat taaaattttt aggtattgat ttcgactcca
     1141 ttttttgccc gttttggttg ttagttcctg acaacgttta tctattcttg taataatttt
     1201 gggattgata tttcgaacta aaatgtccat ggaaattttc ctttcgtatc agtatataat
     1261 ttatgtatat catacaaata tagtatttgt atagctattt ttcgccaaaa cactatacat
     1321 agcctagcca caatggcaaa aaagtgatag caaatttttt tctgagaaac gtgataggca
     1381 cagcttatct agcacctttc gtaagaaagt gataccacgt ttccttatgc tctttcaaaa
     1441 ttcagaaaaa tcagctgtaa aacgagtgca gtccgagtaa gattcaacga aaaaacgggg
     1501 attggggcgc caccaaaata tcgcaacatg ggcccatgtt gctctgctcg caaaagcaaa
     1561 aagaagaata aaaccagcaa tttttattaa tttaaattgc tggttttatt gccagaattg
     1621 ccaccatttt ttctccgtct ttgattgttt ttctatcgat tctgtttctt cagaaagagt
     1681 cgttgattta ttttccgaag attcttccgt ataagtcaac tgtagttgtt cctgcagttt
     1741 ctcgatttgt tggttggctt gcagggtgag ttgttgttgc tggtcgagta atttttgttg
     1801 tgtttctaaa gctagttgaa gtttttcaat ttgcctatct ttttcttcaa tatgattatt
     1861 cttagtttca atctccttga gtaggtaatc ggtaggtaat gaatcaggta attcactagg
     1921 taagttaccc ggctcattac ctgataaaac ctttgtaatt gttgttactg cttctttttt
     1981 caggtagata atatttcctt ttttgtaggt aaaattacta ggtaatttcc tcagttgata
     2041 cttcacttta tcttttgaaa cacctagaat atctgctaat tctttgatag ttttatctgt
     2101 cataaaaacc ccttattctt taaataagtt ttgaagatta tctagtaagc ctttttttaa
     2161 ttctggggga atatcggaat tgttatctgg tatttgttcg ttaatctcct tattttcttt
     2221 attcagatta ttttgttttc tttctagctc ttctaattgt tgtaaaagtt ctaattttcg
     2281 tttctgttct ttgatttttt cttgtaatga agtggggtct ttttcagagt aaatttgttg
     2341 attaactagt tctaaagctt tattttgttc ttcttttgtt ggtgcgtgtt tattaaagtc
     2401 gtctgctttt tttatttcag gtttaaacgt gaattgatag ccaatgacag gttttcctct
     2461 tccttttccg tatttctttt tgattgtcag acctttgaag attgcggtta gttcttggcg
     2521 aataggcttt ataatttttt tatttatatc actttctcta taacttttag ggatatcaag
     2581 taattcatga aagtcttctt ttgaaaaata ggcaattcct ttggttctgt attgttttaa
     2641 taatctaaac atggttttgg aataactgct ttctaattca ttgaattgtt ggagagaata
     2701 tcgaacccat tcttcaagat tattaagtaa gggtaaggct ttctcatgga cttgtatttc
     2761 agcaaaagga atatcagctt ttccatcgat tttaaattga ttaaataaaa caaatcgttc
     2821 acgttgcaaa ccgtcagcac ttcttctacc aaaacgtaaa tccattaatt tgtcatacgt
     2881 tgtttctaaa tcatctatga atcgaacatt tgcagttgct ttataattgc ttaaatcttt
     2941 taattgttcg aatgtaaatt gtactttttt atcgcctacg tcacgcattc tagatactat
     3001 agagaagaat aaattcattt ctactgacgt aaatttgcgt aaaggaatcg tatttaattc
     3061 atggtggtat ttcacaattt catttgccat aaaatcctcc ttcaagatta actacttaac
     3121 aaaattataa agagctttct aataggggtc aagcccctaa ttaaagaccc ctaaaaacag
     3181 acaaaaagac ccccaaaaac agacaaaaag acccctaaaa acagacaaaa agacccctaa
     3241 aaacagacaa aaagaccccc aaaagattct gcacaccttg ggagagtaag catacagccg
     3301 acggtaaaga ggtttaaaaa gaggtttaaa aagagattat aaaagaggag gcaaaatttc
     3361 ccgcctaaaa aactcctgct tttttcctca aacaagttcg cgaatttttc taaactggga
     3421 aactcgctcc ctacggtcac taaaaatgtg tgatcgctac gctctcacat tatactgcgc
     3481 agtcgcctaa aggctccttt gcttaaaaac agttcataaa gaactccttt gaaaagttct
     3541 gagcgtttgt ttaagccgtt ttaagacagt cttagtataa aacccttatc ttgttctcaa
     3601 agcgccttac aggcggtcag ggcaagccct aacaacccta aaatgttcta taagacctct
     3661 aaaattagat ctaaggcgtt ttaaagttgt tttggtataa attatatacc agaacgttta
     3721 aaacgcctta aaacgcaaat tatagccata tgtattttta cggaagccgg cacactcatt
     3781 tgcaaagctg aagctttgca aattcagatt cgctcactcg aaaactgatt tgttttggct
     3841 tggatcgata ggtatatttt ttagaatgat cgctagccaa attttgattt tgttcgctca
     3901 taagtcccac cctttcagta cgtcctacgg acgtatcgtt cgcaatacca ttgtacctaa
     3961 aaaggcacaa tgagtaaagc tcaccaaaag ggcttggcaa gctctatatt tgctagccaa
     4021 atacctacgt atttggtgca aataaccgct tttcaaaggg gcgcaagctc ccccttgaat
     4081 ccccctcaaa acccacgctc cacaatacaa aaaaggctag caaatgctag ccactttttg
     4141 taaagtttcg cttgtttcac cttcggtgaa attattgttt tgtaatatca aacaactatt
     4201 catcaatcag ctttaaaaaa ttcaattggt ttagctgtcc cttctgtccc atcattcgtt
     4261 gtcaaaataa atacgagctt ttttggagaa tccaaactaa aagtgtaatc taattgtttt
     4321 ttattagagc gcagtgttag taaattattt gttgctttgt aaatgaaaac ttgttcattt
     4381 atatttaaat ttttatcaat gatttgaatt ttatgattgt tctcttttac taagatggta
     4441 tattgttcta tattttttga agtatttaaa ttagtgatta ctagacgttc tgaatgatct
     4501 ttagtttgcc aagttcctag aaaaggaatc agatcagtct tttgtatttc ttgttttttt
     4561 gaacaactag ttaagaaaag aactaacact agacccataa ctaaagcaat gggtttattt
     4621 accaatttgt aatggtattg tcccaagtaa aaccacctcc aggtacagga attgtaactg
     4681 gtcctgcatt tgcacttatt acagttgggt agttatacca aggattccac acatagtaag
     4741 tttgataacc accttgattg acccacccaa ataatgcaag tgcatgacgg ctgttactat
     4801 aatttccata accagcagtt cccatataaa tggcatttcc ttttcttagt tgtgtttgga
     4861 cctctgaaag gtttagtatt cgtgctactt ttttaggata aacaccacag taatttgcat
     4921 attttattat ttgatcttga ttaagacttt ttgattcaat ttgactgttg tttaaattag
     4981 gataggtata atgcataatg gctctagctg aagtagcatg tacatctgtt ttgttacata
     5041 agatagcagc ttctacgtaa gcagcacacc acggaaaact tgtttgggtt tctgctatac
     5101 gccaattaat cataataaag ttatctccgg aggagacact ttttacacgt ttaaccgcag
     5161 gaaaattttg ttttttagag aaatttttaa ttttattttt tatatttacg gatataagat
     5221 catttttttc tgtaaaggaa gaaacaccat ttttttctgt acttaaaggt gatttccaaa
     5281 gtagtttaat ttgtccatta tcggaataat aaatgctatt atcttgaaaa aataaggttg
     5341 tatctgttat attactatct actagatttt gaagttcttt tgctaaaaat tgtgaaatac
     5401 ttcctgaata ttctccattt gtattttttt tgacggtata aatatattta atcgtattat
     5461 cagcgtctga aaatactgga aagaaaatag aactatttgc cgtattttct ccatcgagca
     5521 ttttaaatgg cgaaccaaga gtatagttaa tatcagtttc ggtgttattt tccattaaaa
     5581 gaattgaagt tatggagtgt tcaaaatcag ttttcgcaaa attaattgct tgttcttcaa
     5641 ttggttggga gttgatattg aaattagaat tttctgaagc ataggtattt gtaattccta
     5701 tactaaaaat tccaatcatc aaggaaaaga ggagacctag ataaattttc tttttgggtt
     5761 tcaaaataat cacgcctttg tgttaaattt aagtggtata cacctataat taaaatatac
     5821 aatatgcgat aacaaatttt tgttatagtt
//
