LOCUS       NZ_AP026779             6175 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Enterococcus faecium strain NUITM-VRE1 plasmid pNUITMVRE1_6,
            complete sequence.
ACCESSION   NZ_AP026779
VERSION     NZ_AP026779.1
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  JOURNAL   Unpublished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 6175)
  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
            AP026779.1.
            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..6175
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NUITM-VRE1"
                     /db_xref="taxon:1352"
                     /plasmid="pNUITMVRE1_6"
                     /geo_loc_name="Viet Nam:Hanoi"
                     /lat_lon="20.99138062 N 105.86277218 E"
                     /collection_date="2021"
     gene            3..506
                     /locus_tag="OO969_RS16050"
                     /old_locus_tag="NUITMVRE1_31690"
     CDS             3..506
                     /locus_tag="OO969_RS16050"
                     /old_locus_tag="NUITMVRE1_31690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_264879955.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIY"
                     /name="helix-turn-helix domain-containing protein"
     gene            549..719
                     /locus_tag="OO969_RS16055"
                     /old_locus_tag="NUITMVRE1_31700"
     CDS             549..719
                     /locus_tag="OO969_RS16055"
                     /old_locus_tag="NUITMVRE1_31700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            1168..1392
                     /locus_tag="OO969_RS16060"
                     /old_locus_tag="NUITMVRE1_31710"
     CDS             1168..1392
                     /locus_tag="OO969_RS16060"
                     /old_locus_tag="NUITMVRE1_31710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363584.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="class II bacteriocin"
                     /protein_id="WP_002363584.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="class II bacteriocin"
     gene            1412..1699
                     /locus_tag="OO969_RS16065"
                     /old_locus_tag="NUITMVRE1_31720"
     CDS             1412..1699
                     /locus_tag="OO969_RS16065"
                     /old_locus_tag="NUITMVRE1_31720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_002363589.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     gene            2142..2522
                     /locus_tag="OO969_RS16070"
                     /old_locus_tag="NUITMVRE1_31730"
     CDS             2142..2522
                     /locus_tag="OO969_RS16070"
                     /old_locus_tag="NUITMVRE1_31730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_002321381.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            <2551..3453
                     /locus_tag="OO969_RS16075"
                     /old_locus_tag="NUITMVRE1_31740"
                     /pseudo=""
     CDS             <2551..3453
                     /locus_tag="OO969_RS16075"
                     /old_locus_tag="NUITMVRE1_31740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3413..3691
                     /locus_tag="OO969_RS16080"
                     /old_locus_tag="NUITMVRE1_31750"
     CDS             3413..3691
                     /locus_tag="OO969_RS16080"
                     /old_locus_tag="NUITMVRE1_31750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002354385.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002369881.1"
                     /translation="MKEEQTTNKNYRSKTLQDIENEIKKQRAFLAPYTKERIQTTIDSQ
                     VKKFHHALLNQRNKEQKKVIMQRSMDILAPLCCLIMTLLAFWLVWGE"
                     /name="hypothetical protein"
     gene            3698..4387
                     /locus_tag="OO969_RS16085"
                     /old_locus_tag="NUITMVRE1_31760"
     CDS             3698..4387
                     /locus_tag="OO969_RS16085"
                     /old_locus_tag="NUITMVRE1_31760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002369882.1"
                     /translation="MAFYLPYLLIFASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLPG
                     VIFTLSIVLSGLFGVLEGNKRISRSILLGDITQKYEAACDKKKKEQVLTQKMEEFTTCY
                     EEMNDIFVNQEKRLTDKNMEKLTRLYQNLPEKQQKEVQDNYERTKKDVQYFKDTQTEEA
                     CYNLFSDTIPFSTSEQERKERQQSVTYERYKALLQQATNIQNPTKKETALNYLKSVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            5231..6175
                     /locus_tag="OO969_RS16090"
                     /old_locus_tag="NUITMVRE1_31770"
     CDS             5231..6175
                     /locus_tag="OO969_RS16090"
                     /old_locus_tag="NUITMVRE1_31770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /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_264879954.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVEDLKATYEKILSLRFGRRSESGLSYDMFVMFTEFKINGD
                     VENPYVDIRIYEKALPLLNNLDEWVRYSLQQFNELQSGYAKTMFRLLKQYRTKGFAYFS
                     KEDFLELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQIKQ
                     LEKEKEALEKQTESALSEKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     BGC             1..6175
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          5232..6175
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.894"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2552..3450
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.333"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtatgcaacc acaagaaacc tttacaataa aggaattgtc agaacttttt aagatgagta
       61 ggcaagcaat atcgaaacat atccaaaaat tagattcttc catgatagct aaaaatgagc
      121 gtggttataa ggttgtattg cgttctggag tattgcaact tgctcgcaac ttaggcaacc
      181 aaatgttgct agataggttg cacgagtacg aacaagacaa cgataaaaat gttaatatac
      241 caagcaaaaa cgtggttaca aacaagttgc tagatcagtt gcgtgaagaa aatgaatttt
      301 tacgagaaca acttgccctc agagagcaaa ataattctca tatacaaaaa ctactcgacc
      361 agcaacaaca actcacccta caagccaaca aacaaatcga aaaactgcaa gaaaaactac
      421 agttgactta tacagaagaa gctccagaga atgactcaac gactctttct gaagcaacag
      481 aaacaataga caaacaaatt tactgaaaaa aatggtggca actttggaaa taactggagg
      541 gaacattcat gacaagaaaa aatcttctat tcggttctat tttactagga attctaggat
      601 tcagtccgat gttattgtca gtgatcaata aagggaataa acatggtgaa ttgaaattga
      661 atccaaatta ttacaacagt cctaacgaag aattgtttgt aaaagaaaca gataaataat
      721 aaaaaagact gctctttcga gcagccagtt aaaaaataat gagtgtttat tcttgaaaaa
      781 gcaacgcgct tatgaagcgc taccaaaaat ttatcatatt ttattaaaaa taacaaccca
      841 gtaaaaaatg actggtaaaa attcacaaag aaacggaaag aagcaaccgc agaaaatcaa
      901 gcttaaaaag agcttttgac ctagaccaat cgaaaatcac aaagtgagcc tctgtatcgg
      961 ttgatacaag ggctacttgg catagtgtac attatgtcta ctagctgttt aaataactga
     1021 tcttataatt ttatttaaac gattatgaat tcaaaactac tttttatgac gttaatcatt
     1081 gttatataat aaaatgttat ataataaaat tactaagatt atttaatata acaagcaatt
     1141 ttaaaaaaac gaaaaggaaa aacaatcatg aaaaagaaag tattaaaaca ttgtgttatt
     1201 ctaggaatat taggaacttg tctagctggc atcggtacag gaataaaagt tgatgcagct
     1261 acttactatg gaaatggtct ttattgtaac aaagaaaaat gttgggtaga ttggaatcaa
     1321 gctaaaggag aaattggaaa aattattgtt aatggttggg ttaatcatgg tccatgggca
     1381 cctagaaggt agtggtaggg aggttattat aatggatttt actaaagaag aaaaactttt
     1441 aaatgcaatt agtaaagtat acaatgaagc aactatagat gactatcctg acttaaaaga
     1501 aaagctcttt ctttattcta aagaaatcag tgagggaaaa agtgttggtg aagttagtat
     1561 gaaattaagt agttttcttg gaagatatat tttaaaacat aaatttggat tacctaaatc
     1621 tttaatagaa ttacaagaaa ttgttagtaa ggaatctcaa gtatatagag gatgggcttc
     1681 tattggtatt tggagttaat tctttggaat aaaatgaaaa tgggactgaa gaatcaattc
     1741 tgattcatca gtcccataaa ttatagagcc gaaaaattat catatttata gatttattaa
     1801 tagtaaatgg cataagaatc tttgaacaac gaaaaaaatg tagctctacc taattattga
     1861 tttgcaacaa tttcaccttc ggtgaaataa gcgaaacttt acaaaaagtg gctagcaaat
     1921 gctagccttt ttttgtattg tggagcgtgg attttgaggg ggattcaagg gggagcttgc
     1981 gctcctttga caagcggtta tttgcaccaa atacggaggt atttggctag caaatataga
     2041 gcttgccaaa cccttttagt gagctttact cattgtacct ttttaggtac aatggtattg
     2101 cgaacgatac gtccgtagga cgtactgaaa gggtgggact tatgagcgaa caacatcaaa
     2161 atttggctag cgatcattct aaaaaatata cctatcgatc cgagccaaaa caaatcagtt
     2221 ttcgagtgag cgaatccgaa tttgcaaagc tgaagcagtc agctgaagct ttgcaaatga
     2281 gtgtgccggc tttcgtgaaa gccaaggcac aaaacgcgcg tctggtgaca ccgaaagtgg
     2341 cgccagacat tgcccaggca atcgcgcgcg atttagccaa agctggaggg aatatcaatc
     2401 aaattgccaa gtggtgcaat acacaccaac acgacgttgc tcctgatgat gctcaacgtt
     2461 tatccgaaaa cctaaaaatc atgcaaaagg agctacaaaa gatatggcaa cagttaaagt
     2521 aagccgaacc acttcttgta gccgagcgat caattacgcc gaaccacttc ttgtagccga
     2581 gcgatcaatt acgccgaacc acgagcaacc gtcaaaacag ggataaactg tgacattgat
     2641 tatgccaaaa gcgaaatgaa acaaattcgc atgctgtatg gaaaagacga tcgtgtacaa
     2701 gcacacttat tgatccagtc ttttcgacca ggagaaatta ccgctgaaaa agccaatcaa
     2761 ctaggggcag agtatgcgaa aaaaatagcc cctgaccacc aaatcgcgat ttacacacat
     2821 acagacaaag accatattca taaccacatt gtcattaact ccgtcaatct ggaaactggg
     2881 aacaaatttc aagcccatgg gcaagcattt ttaaacaaat gttatgacct aaatgacgag
     2941 atttgtcttg aacatgactt aacaatcact gaacgaggga agaaacccga aaaacgaacc
     3001 atgtctgaaa tcaaattaaa agaaaaaaat gaacctgttt ggaaagacga aattcggttt
     3061 gcgattgatc aaacaatgaa aaacaaaaaa actcgaacgt ataaccaatt ttgtgattct
     3121 cttaaaacat tcggcattca ttgcttgaat cgtgggaaaa attttactta cgaattgatc
     3181 cacaaaaaga aaaaagtacg atccaacaaa ctaggaaagg attacgaaaa ggagacgatt
     3241 ttacatgagc tggacagacg agaacgagcc tacaatcaac aacgaaccaa cgagctacga
     3301 agagctcgag ctagcattcg cgaaactgca aaagaagtac gaagagaaca acgaactctt
     3361 acgactgaac aaccggaaat tagaccgact cgaagaaacc atgaccaaca cgttgaaaga
     3421 ggagcagact accaacaaga attatcgttc taaaacgtta caagacatag aaaatgaaat
     3481 aaagaaacaa cgtgcttttc ttgcacctta taccaaagaa agaatacaaa ctacaattga
     3541 ttcacaagtc aaaaaattcc accatgcgct attaaaccag cgaaataaag aacagaaaaa
     3601 agtaattatg cagcgatcaa tggatattct tgccccctta tgttgcttaa tcatgacact
     3661 gttagccttt tggctggtat ggggagaata aatagaaatg gcattctatt taccctatct
     3721 actcattttt gccagtattt taggaattat ttggcttagc tataaggctt atcaaacaag
     3781 atattcatta aaaggctcta aaattcgatt taagaggttt ttattgccag gggttatatt
     3841 tacattatca atcgttttaa gtggtttatt cggcgtttta gagggaaata aacgtatttc
     3901 aagaagtatt ttattagggg atatcactca aaagtatgaa gcagcatgtg ataaaaagaa
     3961 aaaggagcaa gtgttaacac aaaaaatgga agagtttacc acttgttatg aggaaatgaa
     4021 cgatattttt gtgaatcaag aaaaacgttt gacggataaa aacatggaaa aactcactcg
     4081 tctttatcaa aacttgccag aaaaacagca aaaagaggtt caagacaact atgagcgaac
     4141 caaaaaagac gtgcaatatt ttaaagatac gcagacagaa gaagcttgtt ataatttatt
     4201 cagtgataca atcccttttt caactagtga acaggaacga aaagaacggc aacaatcagt
     4261 tacctacgaa cgttataaag cactgcttca gcaagcaacg aacatacaaa atccaacgaa
     4321 aaaagaaacg gcattaaatt atctaaaaag tgtcaaggaa tggttagatc agcaacagca
     4381 aaattgaatt tgatcggcaa tcatgttaaa ctaaacatgc aaatgatcaa acattagata
     4441 cacgaaagcc ccagagaggt cggattctct ggggcttttt ttcaggttga tgtcgccttt
     4501 attgatttta cttcttgttt cggttattca accaataact gaataaagag acacaaactt
     4561 ctataagaag ggggcaaatg aacaattcaa acattagata cacctccttc cagtcgcaag
     4621 actgtcggat aggcgacaag ttattatatc ttaaaaaatt aaacttgtgt ggtgttttta
     4681 agtatcgctt attttagggt tgttagggct tgccctgacc gcctgtaagg cgctttaaag
     4741 ctagataagg atttttatcc aagactgtct taaaacggct tagataagca ttcagaaccg
     4801 ctcaaaggcc tctttaccaa catgttttta gcaaaggagc ctttaggcga ctgcgcagta
     4861 caatgtgaga gcgtagcgat cacacctttt tggcgaccgt aggaagcaag gttttggatt
     4921 ggcagttttg aaaaatgcgc gaacctgttt aaagaaaaaa gaagtggttt ttaggcggga
     4981 aaattagccc ccctcttttt atatctcttt ttaaacctct ttttaaacct ctttaccgta
     5041 agctgtgtcc ttactctacc aatggataca gaatgttatg aaggacattt tgtctgttta
     5101 tgaaggacat tttgtctgtt tatgaaggac attttgtctg tttatgaagg acattttgtc
     5161 tgtttgaacg tcaaatatga atgtcttgac atttaaaaaa tgtcattcat aattggattg
     5221 aggtgattat atggctaatg agattgtaaa ataccaccat gaattaaata caattccttt
     5281 aagaaaattt acaccggttg aaatgaattt gtttttttcc atcgtgtcta gaatgcgtga
     5341 aaaaggggat aagacagttc gttttacgtt tgaccaacta aaagatttaa gtaactacaa
     5401 agcaactgca aatgtacgat ttgtagaaga tttaaaagca acttatgaaa aaatcttatc
     5461 tttacgcttt ggtcgtagaa gtgagtctgg gctttcttac gatatgtttg taatgtttac
     5521 agaatttaaa atcaacgggg acgtagaaaa tccttacgta gatatacgaa tttacgaaaa
     5581 agcactgcct ttgttaaata atttagacga gtgggtacgc tattctttac aacaattcaa
     5641 cgagctacaa agtggctatg caaagactat gtttcgtctg ttaaagcaat acagaaccaa
     5701 aggtttcgca tatttctcca aagaagactt tcttgaatta ttagatattc ctaaaagtta
     5761 taagcaacct gatatagata aacgagttat aaaacctata cgtcaagaac taactgcaat
     5821 cttcaaagga ctaacaatca aaaagaaata cggaaaagga cggggaaaac ctgttattgg
     5881 ctatcaattt acgttcaaac ctgagatcaa aaaagcagac gactttaaca aacatgcacc
     5941 aaccaaagaa gaccaaaata aagcattggc tttagctgat aaacaaaaag aatacgaaga
     6001 acccgctaca acaattaacg aaaaaatcaa acagaagaaa cgagaacttg aactcctcca
     6061 acaaatcaaa caactagaaa aagagaaaga agctcttgaa aaacaaacag agtccgcact
     6121 ttcggaaaaa gagaaaaaaa gtttattatc tgatttagat aatttattcc agtag
//
