LOCUS       NZ_AP026777             6776 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Enterococcus faecium strain NUITM-VRE1 plasmid pNUITMVRE1_4,
            complete sequence.
ACCESSION   NZ_AP026777
VERSION     NZ_AP026777.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00533729
            Assembly: GCF_025998395.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1
  AUTHORS   Suzuki,M., Hashimoto,Y. and Tomita,H.
  TITLE     Complete genome sequence of Enterococcus faecium NUITM-VRE1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6776)
  AUTHORS   Suzuki,M., Hashimoto,Y. and Tomita,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-SEP-2022) Contact:Masato Suzuki National Institute of
            Infectious Diseases, Antimicrobial Resistance Research Center; 4-2-1
            Aobacho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 2.1.1
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Illumina HiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/27/2023 03:20:54
            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)                     :: 3,228
            CDSs (total)                      :: 3,138
            Genes (coding)                    :: 2,975
            CDSs (with protein)               :: 2,975
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 65 of 163
            Pseudo Genes (incomplete)         :: 91 of 163
            Pseudo Genes (internal stop)      :: 36 of 163
            Pseudo Genes (multiple problems)  :: 25 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026777.1.
            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..6776
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NUITM-VRE1"
                     /db_xref="taxon:1352"
                     /plasmid="pNUITMVRE1_4"
                     /geo_loc_name="Viet Nam:Hanoi"
                     /lat_lon="20.99138062 N 105.86277218 E"
                     /collection_date="2021"
     gene            complement(<2..1126)
                     /gene="tnpB"
                     /locus_tag="OO969_RS15965"
                     /pseudo=""
     CDS             complement(<2..1126)
                     /gene="tnpB"
                     /locus_tag="OO969_RS15965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349331.1"
                     /note="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="IS200/IS605 family element RNA-guided
                     endonuclease TnpB"
                     /name="tnpB"
     gene            complement(1143..1547)
                     /gene="tnpA"
                     /locus_tag="OO969_RS15970"
                     /old_locus_tag="NUITMVRE1_31530"
     CDS             complement(1143..1547)
                     /gene="tnpA"
                     /locus_tag="OO969_RS15970"
                     /old_locus_tag="NUITMVRE1_31530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002287522.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS200/IS605-like element ISEfa4 family
                     transposase"
                     /protein_id="WP_264879953.1"
                     /translation="MNADTNNHSVFLLYYHLVLVTKYRRQVIDDEISDYAKTTFERISE
                     SYHITLVEWNHDKDHVHIMFKAQPKTELTKFINAYKSASSRLIKRDFPRVKQFLWKEMF
                     WSKSFCLLTTGGAPIDVIKKYIQNQGNNHK"
                     /name="tnpA"
     gene            complement(1759..2175)
                     /locus_tag="OO969_RS15975"
                     /old_locus_tag="NUITMVRE1_31540"
     CDS             complement(1759..2175)
                     /locus_tag="OO969_RS15975"
                     /old_locus_tag="NUITMVRE1_31540"
                     /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_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(2177..2458)
                     /locus_tag="OO969_RS15980"
                     /old_locus_tag="NUITMVRE1_31550"
     CDS             complement(2177..2458)
                     /locus_tag="OO969_RS15980"
                     /old_locus_tag="NUITMVRE1_31550"
                     /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_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            complement(2834..3358)
                     /locus_tag="OO969_RS15985"
                     /old_locus_tag="NUITMVRE1_31560"
     CDS             complement(2834..3358)
                     /locus_tag="OO969_RS15985"
                     /old_locus_tag="NUITMVRE1_31560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /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_044383356.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTENHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KAEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(3375..4343)
                     /locus_tag="OO969_RS15990"
                     /old_locus_tag="NUITMVRE1_31570"
     CDS             complement(3375..4343)
                     /locus_tag="OO969_RS15990"
                     /old_locus_tag="NUITMVRE1_31570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            complement(5533..5736)
                     /locus_tag="OO969_RS15995"
                     /old_locus_tag="NUITMVRE1_31580"
     CDS             complement(5533..5736)
                     /locus_tag="OO969_RS15995"
                     /old_locus_tag="NUITMVRE1_31580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002307460.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002321382.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            complement(5748..6281)
                     /locus_tag="OO969_RS16000"
                     /old_locus_tag="NUITMVRE1_31590"
     CDS             complement(5748..6281)
                     /locus_tag="OO969_RS16000"
                     /old_locus_tag="NUITMVRE1_31590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002334266.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     Typing          complement(3380..4343)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtcttagacc ttcggtcaga atattgatac tagcattgat atcacgatca tgatgagtat
       61 gacaaacagg acaagtccat tctcgaattt caagagattt cttgccatct ttatgtccgc
      121 actctgaaca aatctgacta gacggaaacc atttatctac tttgatgatt tttcgtccat
      181 accagtcagc cttgtattgt aatttagtca caaactttga ccaagaaaca tcagaaatac
      241 ttttagctaa tttatgattt cgcaacatac cttttgtgtt taagtcttca atacagataa
      301 tatcgtgatt tttgatcatt tctgtactca acttattcag aaaatcagta cgttgattca
      361 ttactttttc atgcaatcta gctactttgc gtttttgttt ttgataattt ttagcttcaa
      421 atagattggt acctttattt ttagccaata aagcacgcct agacaatttg cgttgttcac
      481 gctttagttt cttttccatt ttggacgtga atttattatt atcaattttt tgtccatcag
      541 aaagaatcgc aaagtccata atacctaagt caataccaat tgtggaatta gttttaggta
      601 attcgataat ttcttcttta cacaacaaag aaatatagta tttaccgcta gaatgacgtg
      661 atattgtagc agatttgata atcccttttg gttgtctatg aagcttaatt cttactaatg
      721 acttcaattt aggaactttg atgaatttac tatcaatcaa agcaactgta ccattttgat
      781 tattcgttgt ataactctga acaggatttt tcttactttt gaaacgtgga aatccaacgg
      841 atttatcccg aaaaaaattc ttgtatgctt tatctaaatt aagttgggca ttggctaaag
      901 caaggctatc aatttctttc aaaaacggaa attctttctt gtatttagct ggtgtcggaa
      961 aagtcatttt tttagaagaa tcatttttaa cttcttcata cgcctttttt cggtcatcaa
     1021 gcattagatt gtagacctta cggacacaac caaaagattt ggcaaagaag atttcttgtt
     1081 cctctgttgg atagattctg aatttgtatg cttttagttg ttccataaag ttcacctact
     1141 ttctatttat gattgtttcc ttgattttgg atatacttct taatcacatc aattggtgcg
     1201 ccaccagttg tcagaagaca aaaactttta gaccagaaca tttctttcca aagaaattgt
     1261 ttgactcttg gaaagtcacg ttttatcaat cttgagctgg cacttttata ggcattgatg
     1321 aattttgtca attctgtttt aggttgagct ttgaacataa tatgaacgtg gtctttatca
     1381 tgattccact ccactaaagt aatgtgatac gattctgaaa ttctttcaaa agtagttttg
     1441 gcataatcag atatttcatc atcaatcact tgtctacgat atttcgttac taaaacaagg
     1501 tggtaataaa gaagaaatac tgaatgatta tttgtatcgg cattcatcac ccacctatag
     1561 aggatgggcg acttctgcct aattctgtta aataaccgat acttggggat tggggtagcg
     1621 cctcaaaata caaaaagaag aagttgcata agcggatttt tctttttttt cgcaagttgg
     1681 taccaacttg caaatcttgc tggaagactg atccctaaaa agaaatcgag gaattttttt
     1741 agggatcggt ttcttttttt atctttttag aaagtttgtt gggtcaaaat ttccagaagt
     1801 aaaggtttga ttggtttctt tttgacgatt tttgggttga tttcgtcggg aaggattgag
     1861 ttgattttca attttttctt tcacttcttg atacacttta gaatttgtac cgataagaac
     1921 accagtatct tttagatata aatcagcaaa ttctgccatg atttctgtca tgatagaaat
     1981 ttcttttccc atggcattga gttttgcttg gttactggtt gtggttgtat tggtatcagg
     2041 ttcataactc atacataaaa aacgaatggc ttctgaataa ttgttgacgt ctggattttt
     2101 ttcgatgatg gaatctaaaa cgtcaacgtg actgggataa agggttacgt gtttttgaac
     2161 agaagttttt ctcatgttat attcctccga taagtgtttc aatgagttgg ttgtttgtgt
     2221 gaacatagtc attcagtatg ttcgtatttt ctgtttgaat ggcaataaat ttttcgagta
     2281 ataaatcgaa ttgatctttt ttgtaattca taagttgacg gtcaaaatca ctttcgatta
     2341 gaacttttag atatttattt cgactccatt ttttgcccgt tttggttgtg agttcctgac
     2401 aacgtttatc tattcttgca ataattttgg gattgatatt tcgaactaaa atgtccatgg
     2461 aaattttcct ttcgtatcag cgtataattt atgtatacca tacaaatata gtatttgtat
     2521 agctattttt cgccaaaaca ctatacatag cctagccaca atggcaaaaa agtgatagca
     2581 aatttttttc tgagaaacgt gataggcaca gcctatctag cacctttcgt aagaaagtga
     2641 taccacgttt ccttatgctc tttcaaaatt cagaaaaatc agctgtaaaa cgagtgcagt
     2701 ccgagtaaga ttcaacgaaa aaacggggat tggggcgcca ccaaaatatc gcaacatggg
     2761 tccatgttgc tctgctcgca aaagcaaaaa gaagaataaa accagcaatt tttattaatt
     2821 taaattgctg gttttattgc cagaattgcc accatttttt ctccgccttt gattgttttt
     2881 ctatcgattc tgtttcttca gaaagagtcg ttgatttatt ttccgaagat tcttccgtat
     2941 aagtcaactg tagttgttcc tgcagtttct cgatttgttg gttggcttgc agggtgagtt
     3001 gttgttggtg gtcgagtaat ttttgcattt gttttatttg ctcgtctttt tcttgtagtt
     3061 gcatatcttt ttgatttaac tgttgttcta ggagagaaag gacttctaat tcgggaactt
     3121 ggttggcgtt tttgtggttt tcggttttcg ttttttcgcc aactagttgt tgatttgagt
     3181 tttcgttttc gttaaaaaac attgatttta tagccttttg tccggtttca ttaatcacaa
     3241 acttgtttcc gattttcgaa aaccaaagtt ttcgattttc gtcagaaact tttttgttaa
     3301 ttgctgtttt actaactcct aattcttcag caagttcttt gattgttttt tctgtcataa
     3361 aatctaaaaa cccctcaatc tttgaataag ttttgaagat tgtctaataa gtcttttttt
     3421 agttctgaag gaatatcgga atttatctct gatttttgtg cattattttc tttattttgg
     3481 gtattttgtt ctctttctaa cttttctaac tgttgtaaaa gttccaattt tcgcttttgt
     3541 tctttgattt tttcttgtaa tgaagtaggt gctttttcag attgaacttg ttggttagct
     3601 agttctaatg ctttgttttg ttcttctttt gttggggcat gtttgttaaa gtcgtctgat
     3661 ttttttatct caggtttaaa tgtaaattga tagccaatga caggctttcc ccgtcctttt
     3721 ccgtatttct ttttgattgt taaaccttta aagattgcgg ttagttcttg tcgtattgga
     3781 ttgaacacac gttgatcaat cgtaccttgg ttgtaacttt taggaatatc aagtaattca
     3841 tgaaagtctt cttttgaaaa ataagcgaaa cctttggttc tgtattgttt tagtaatcga
     3901 aacattgttt ttgaataact gctttctaat tcattgaatt gttggagaga atagcgcacc
     3961 cattcttcaa gattattaag taagggtaag gctttttcat gaacttgtat ttcagcaaaa
     4021 ggaatatcag attttccgtc gattttaaat tgattaaata aaacaaaacg ttcacgttgc
     4081 aaaccgtcag cacttcttct accaaaacgt aaatccatta atttgtcata cgttgtttct
     4141 aaatcatcta tgaatcgaac atttgcagtt gctttataat tgcttaaatc ttttaattgc
     4201 tcgaatgtaa attgtacttt tttatcacct acatcacgca ttcttgatac gatagaaaag
     4261 aacaaattca tttcgactgg tgtaaatttt cgcaacggaa ttgtatttaa ttcatgatga
     4321 tactttacga tttcattaga catatttaaa atagctcctt tcttactcgc acaagagata
     4381 cacgttatga aatacaaaat gcctgtttat ctacatctta tattaacatc gtcgatgtac
     4441 taattcaatg tacaaacaga caaaacgatg tagataaaca gacaaaacga tgtagataaa
     4501 cagacaaaac gatgtagata aacagacaaa acgatgtaga taaaagcgtc attcccttgg
     4561 gagagtaagg atatagccga cggtaaagag gtttaaaaag aggtttaaaa agagattata
     4621 aaagaggggg acaaaatttc ccgcctaaaa aaccacttct tttttctcca aacagattcg
     4681 cgcatttttc tcaactggga atcttactcc ctacagtcgc ttaaaaaggt gtgatcgctc
     4741 tgctctcaca ttatactgcg cagtcgcttc cggctccttt gctaaaaatg ttcataagga
     4801 actctttgag aagctatgag ccttcgtttg agacgtttta agacagtctt agtataaatc
     4861 ccttatcttg ttcttaaagc gccttacagg cggtcagggc aagccctaac aaccctaaag
     4921 ttgtctgaat gccctctaaa attcgattta agcactctta aacctactct tatatattta
     4981 tatacttaga cgtttcaaac gtcttaaaac gcaaattaga gcttgataaa gatatttgct
     5041 cgtgtgccga cttttttaaa agtctaggca cacgccatga caaagctgaa ataaactgct
     5101 tcagctttgt catggcggat tcgctcactt gaaaaagtgt tcatttcgct cgattattag
     5161 catatatttt ttaacttttt ttgctagcca aattttgcat tagttcgctc ataaatccca
     5221 ccctttcagt acgtcctacg gacgtatcgt tcgtaatgtg aaagtacctt taaaggtact
     5281 ttctacaaaa ctcactaaag tgtttggcaa gctctatatt tgctagccaa atacctccgt
     5341 atttggtgca aataaccgct tgtcaaagga gcgcaagctc ccccttgaat ccccctcaaa
     5401 atccacgctc cacaatacaa aaaaaggcta gcatttgcta gccacttttt gtaaagtttc
     5461 gcttatttca ccgaaggtga aattgttgct ttgtaatatt caaacaaccc tattcttcta
     5521 aaatgtatcg atttattttt ttttagactt tattatgtct aagacaacta agattaacac
     5581 taaaaataaa ccagatttgt ataattgccc tccgcttagc atattaacaa ttatagcaac
     5641 agctatagca aatataaaaa tacgaatagt agctatttgc ggattctttt tagtaaatgt
     5701 ttttaatgat tttaatgatt tagatatcaa aaacatcact ccttaactta taacgttgaa
     5761 tatctagtag ctacaactct tccagctgca tcatatcccc tttggtaata aaatccaatc
     5821 cagccattac catttttgtc ccattctttt gcaactgcat tccctggaga agcacctttt
     5881 ttagtccaac ttgcacctgt taacaaagca ccaattgccc aacctgggat accaaacata
     5941 gaagtgctag ctttccctcc tgcccaaaag gcagcattaa tagcattagc agctactcca
     6001 gtggttacag caatatttgt atattccttt ttgccccatc ttgcaactgc agctcttgtc
     6061 atgatatctg aagaatttgc aaaatcttcc gcactataac catcctcata tttagttacg
     6121 accataccat cttcagtgta ctcaataact acattttcag tagcattgtt ttcgtttaat
     6181 gataccactt gggaattttc tgaagcataa actatagtag ttgacggtaa aacaactgcc
     6241 ccaatagtta acaaagctac ccctaaagta aattttttca tagaatttcc tcctgataca
     6301 gaaaaatata tagaaaacgt tttctttgtg aaaatcataa aacaaaaggt ataggcttgt
     6361 caatatttta tttagtaaag ataatttata tttttgataa tgtggtatag ttagaatgca
     6421 ttaggaaaat atgttatatt aaattcttgt tgacataatg tcgactatgc caagtagccc
     6481 ctctaccaat ggatagagac gctcactttg tgatttttaa ttggtctagc tagttactag
     6541 cttctaatgc ttgattttac gcgatttctc ttttttagtt ctttgtgcat ttttatctgt
     6601 cattttttaa agacttgtta tttttgagag gatttgatat gctttttttg tctttctcta
     6661 gttcttcact ttgtaatatt tttatgttga tgaataggat aatctcattt tgggctgctc
     6721 gtgagagcag tctttttttg tttcagggta cgtcctattc tttggatttc cgcgct
//
