LOCUS       NZ_AP028418             6303 bp    DNA     circular CON 01-NOV-2023
DEFINITION  Enterococcus faecium strain 8419 plasmid pSU8419_3, complete
            sequence.
ACCESSION   NZ_AP028418
VERSION     NZ_AP028418.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00623430
            Sequence Read Archive: DRR488523, DRR488528
            Assembly: GCF_033130085.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1
  AUTHORS   Tanabe,M., Denda,T., Natori,T., Horiuchi,K., Koide,S., Nagano,Y. and
            Nagano,N.
  TITLE     Novel genomic island carrying a new vanD allele in a
            vancomycin-resistant Enterococcus faecium clinical isolate belonging
            to a pandemic CC17 clone in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6303)
  AUTHORS   Tanabe,M. and Nagano,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2023) Contact:Mizuki Tanabe Shinshu University
            Graduate School of Medicine, Health and Medical Sciences; 3-1-1
            Asahi, Matsumoto, Nagano 390-8621, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 360x
            Sequencing Technology :: Oxford Nanopore Technologies GridION;
            Illumina NovaSeq 6000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/01/2023 10:57:53
            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)                     :: 3,064
            CDSs (total)                      :: 2,972
            Genes (coding)                    :: 2,844
            CDSs (with protein)               :: 2,844
            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)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 49 of 128
            Pseudo Genes (incomplete)         :: 79 of 128
            Pseudo Genes (internal stop)      :: 32 of 128
            Pseudo Genes (multiple problems)  :: 25 of 128
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028418.1.
            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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="8419"
                     /isolation_source="Necrosectomy"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pSU8419_3"
                     /geo_loc_name="Japan:Nagano, Matsumoto"
                     /collection_date="2022-08-31"
     gene            1..951
                     /locus_tag="R9B63_RS15250"
                     /old_locus_tag="SUGS_400010"
     CDS             1..951
                     /locus_tag="R9B63_RS15250"
                     /old_locus_tag="SUGS_400010"
                     /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_033642128.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKEALEKQTESALSKKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            972..1505
                     /locus_tag="R9B63_RS15255"
                     /old_locus_tag="SUGS_400020"
     CDS             972..1505
                     /locus_tag="R9B63_RS15255"
                     /old_locus_tag="SUGS_400020"
                     /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="DUF536 domain-containing protein"
                     /protein_id="WP_002321384.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1521..1691
                     /locus_tag="R9B63_RS15260"
                     /old_locus_tag="SUGS_400030"
     CDS             1521..1691
                     /locus_tag="R9B63_RS15260"
                     /old_locus_tag="SUGS_400030"
                     /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            2141..2674
                     /locus_tag="R9B63_RS15265"
                     /old_locus_tag="SUGS_400040"
     CDS             2141..2674
                     /locus_tag="R9B63_RS15265"
                     /old_locus_tag="SUGS_400040"
                     /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"
     gene            2686..2889
                     /locus_tag="R9B63_RS15270"
                     /old_locus_tag="SUGS_400050"
     CDS             2686..2889
                     /locus_tag="R9B63_RS15270"
                     /old_locus_tag="SUGS_400050"
                     /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            3211..3591
                     /locus_tag="R9B63_RS15275"
                     /old_locus_tag="SUGS_400060"
     CDS             3211..3591
                     /locus_tag="R9B63_RS15275"
                     /old_locus_tag="SUGS_400060"
                     /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            3573..4487
                     /locus_tag="R9B63_RS15280"
                     /old_locus_tag="SUGS_400070"
     CDS             3573..4487
                     /locus_tag="R9B63_RS15280"
                     /old_locus_tag="SUGS_400070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_002321380.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRT
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPNHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKTEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYTQFCDSLKTFGIHCLNRGKNFTYELVHKKKKVRS
                     NKLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTFTPEQSEI
                     RPTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4732..5421
                     /locus_tag="R9B63_RS15285"
                     /old_locus_tag="SUGS_400080"
     CDS             4732..5421
                     /locus_tag="R9B63_RS15285"
                     /old_locus_tag="SUGS_400080"
                     /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_002321377.1"
                     /translation="MAFYLPYLLISASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLVG
                     VIFALSIVLSGLFGVLEGNKRVSRSILLGDITQKYEAACDKKKKEQALAQKMEEFTACY
                     EDMNNIFVDQEKRLTDKNMKKLTRFYQNLPEKQQKEVQEKYEQVKKDVQYFKDTQTEEA
                     CCNLFSDTIPFSTSEQERKERQQSVTYERYETLLQQATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     Typing          3..951
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3574..4484
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggcaaatg aaatcgtgaa ataccatcat gaattaaata ccattccgtt gcggaaattt
       61 acaccagttg aaatgaatct atttttctct attgtgtcta gaatgcgcga aaaaggcgat
      121 aaaacagtcc gtcttacttt tgaccaacta aaagatttaa gtaattataa agcaactgct
      181 aataatcgtt tcattaatga tttagaaatg acttatgata aattaatgga tttacgtttt
      241 ggtaaaagaa gtgctaatgg gctcgatata gatagattcg ttatgtttag tgagtttaaa
      301 atacgtggaa ctgctaaaga tccatatgta gacatacaag tttacgaaaa agctttacct
      361 ttactaaaca atttagatga gtgggttcgc tattcactcc aacaatttaa cgaattacaa
      421 agtagctatg caaagactat gtttcgatta ctaaaacaat atcgaactaa aggttttgct
      481 tatttttcta aagaggattt tcatgaacta ttagatattc caaaaagtta ctggaacaac
      541 caagcaaacg ttgataatcg tgttataaag cctatacgac aggaattaac cgcaatcttc
      601 aaaggattat caatcaaaaa gaaatacgga aaagggcgag gaaaacctgt cgttggctat
      661 caatttacgt ttaaaccaga aatcaaaaaa gcagatgatt ttaataaaca tgcaccaacc
      721 aaagaagaac aaaataaagc attggcttta gctgataaac aaaaagaata cgaagaacct
      781 gctacaacaa ttaacgaaaa aatcaaacag aagaaacgag aacttgaact cctccaacaa
      841 atcaaacaac tagaaaaaga gaaagaagct cttgaaaaac aaacagagtc cgcactttcg
      901 aaaaaagaga aaaaaagttt attatctgat ttagataatt tattccagta gcaacctagg
      961 aggcaaccag tatgcaacca caagaaacct ttacaataaa ggaattgtca gaacttttta
     1021 agatgagtag gcaagcaata tcgaaacata tccaaaaatt agattcttcc atgatagcta
     1081 aaaatgagcg tggttataag gttgtattgc gttctggagt attgcaactt gctcgcaact
     1141 taggcaacca aatgttgcta gataggttgc acgagtacga acaagacaac gataaaaatg
     1201 ttaatatacc aagcaaaaac gtggttacaa acaagttgct agatcagttg cgtgaagaaa
     1261 atgaattttt acgagaacaa cttgccctca gagagcaaaa taattctcat atacaaaaac
     1321 tactcgacca gcaacaacaa ctcaccctac aagccaacaa acaaatcgaa aaactgcaag
     1381 aaaaactaca gttgacttat acagaagaag ctccagagaa tgactcaacg actctttctg
     1441 aagcaacaga aacaatagac aaacaaattg atactgaaaa aaaatggtgg caactttgga
     1501 aataactgga gggaacattc atgacaagaa aaaatcttct attcggttct attttactag
     1561 gaattctagg attcagtccg atgttattgt cagtgatcaa taaagggaat aaacatggtg
     1621 aattgaaatt gaatccaaat tattacaaca gtcctaacga agaattgttt gtaaaagaaa
     1681 cagataaata ataaaaaaga ctgctctttc gagcagccag ttaaaaaata atgagtgttt
     1741 attcttgaaa aagcaacgcg cttatgaagc gctaccaaaa atttatcata ttttattaaa
     1801 aataacaacc cagtaaaaaa tgactggtaa aaattcacaa agaaacggaa agaagcaacc
     1861 gcagaaaatc aagcttaaaa agagcttttg acctagacca atcgaaaatc acaaagtgag
     1921 cctctgtatc ggttgataca agggctactt ggcatagtcg acattatgtc aacaagaatt
     1981 taatataaca tattttccta atgcattcta actataccac attatcaaaa atataaatta
     2041 tctttactaa ataaaatatt gacaagccta taccttttgt tttatgattt tcacaaagaa
     2101 aacgttttct atatattttt ctgtatcagg aggaaattct atgaaaaaat ttactttagg
     2161 ggtagctttg ttaactattg gggcagttgt tttaccgtca actactatag tttatgcttc
     2221 agaaaattcc caagtggtat cattaaacga aaacaatgct actgaaaatg tagttattga
     2281 gtacactgaa gatggtatgg tcgtaactaa atatgaggat ggttatagtg cggaagattt
     2341 tgcaaattct tcagatatca tgacaagagc tgcagttgca agatggggca aaaaggaata
     2401 tacaaatatt gctgtaacca ctggagtagc tgctaatgct attaatgctg ccttttgggc
     2461 aggagggaaa gctagcactt ctatgtttgg tatcccaggt tgggcaattg gtgctttgtt
     2521 aacaggtgca agttggacta aaaaaggtgc ttctccaggg aatgcagttg caaaagaatg
     2581 ggacaaaaat ggtaatggct ggattggatt ttattaccaa aggggatatg atgcagctgg
     2641 aagagttgta gctactagat attcaacgtt ataagttaag gagtgatgtt tttgatatct
     2701 aaatcattaa aatcattaaa aacatttact aaaaagaatc cgcaaatagc tactattcgt
     2761 atttttatat ttgctatagc tgttgctata attgttaata tgctaagcgg agggcaatta
     2821 tacaaatctg gtttattttt agtgttaatc ttagttgtct tagacataat aaagtctaaa
     2881 aaaaaataaa tcgatacatt ttagaagaat agggttgttt gaatattaca aagcaacaat
     2941 ttcaccttcg gtgaaataag cgaaacttta caaaaagtgg ctagcaaatg ctagcctttt
     3001 tttgtattgt ggagcgtgga ttttgagggg gattcaaggg ggagcttgcg ctcctttgac
     3061 aagcggttat ttgcaccaaa tacggaggta tttggctagc aaatatagag cttgccaaac
     3121 ccttttagtg agctttactc attgtacctt tttaggtaca atggtattgc gaacgatacg
     3181 tccgtaggac gtactgaaag ggtgggactt atgagcgaac aacatcaaaa tttggctagc
     3241 gatcattcta aaaaatatac ctatcgatcc gagccaaaac aaatcagttt tcgagtgagc
     3301 gaatccgaat ttgcaaagct gaagcagtca gctgaagctt tgcaaatgag tgtgccggct
     3361 ttcgtgaaag ccaaggcaca aaacgcgcgt ctggtgacac cgaaagtggc gccagacatt
     3421 gcccaggcaa tcgcgcgcga tttagccaaa gctggaggga atatcaatca aattgccaag
     3481 tggtgcaata cacaccaaca cgacgttgct cctgatgatg ctcaacgttt atccgaaaac
     3541 ctaaaaatca tgcaaaagga gctacaaaag atatggcaac agttaaagta agtcgaacca
     3601 cttcatgtag ccgagcaatc aattacgcag aaccacgagc aaccgtcaaa acaggaataa
     3661 actgtgacat tgattatgcc aaaagtgaaa tgaaacaaat acgcacgctt tatggaaaag
     3721 acgatcgtgt acaagcacac ttattgattc agtcctttcg accaggagaa attaccgctg
     3781 aaaaagccaa tcaactaggg gcagagtatg cgaaaaaaat agcccctaac caccaaatcg
     3841 cgatttacac acatacagac aaagaccata ttcataatca cattgtcatt aactccgtta
     3901 atcttgaaac tgggaaaaaa tttcaagccc atgggcaagc atttttaaac aaatgttatg
     3961 acctaaatga cgagatttgt cttgaacatg acttaacaat cacggaacga ggaaagaaaa
     4021 ccgaaaaacg aaccatgtct gaaattaaat taaaagaaaa aaatgaaccg gtttggaaag
     4081 acgaaattcg gtttgcgatt gatcaaacaa tgaaaaacaa aaaaactcga acgtataccc
     4141 aattttgtga ttcacttaaa acattcggca ttcattgctt gaatcgcgga aaaaatttta
     4201 cttacgaatt ggtccacaaa aagaaaaaag tacgatccaa caaactagga aaggattacg
     4261 aaaaggagac gattttacat gagctggaca gacgagaacg aacctacaat caacaacgaa
     4321 ccaacgagct acgaagagct cgagctagca ttcgcgaaac tgcagaagaa gtacgaagag
     4381 aacaacgaac ttttacgcct gaacaatcgg aaattagacc gactcgaaga aaccatgaac
     4441 aacacgttga acgaggaaca gaccaccaac aagaattatc gctctaaaac gttaaaagac
     4501 atcgaaaacg aaataaagag acaacgtgcc tttcttgcgc cttataccca agaaaggata
     4561 caaactacga tggattcaca agtcaaaaaa ctccaccaag cgctattaga ccagcgaaac
     4621 caagaacaaa aaaaggcttt aattcaacga tcgatggata ttcttgcccc cttatgttgc
     4681 ttagtactaa cattattagc cttttggttg gtatggggag aataaacaga catggcattc
     4741 tatttaccct atctactcat ttctgccagt attttaggaa ttatttggct tagctataag
     4801 gcttatcaaa caagatattc attaaaaggc tctaaaattc gatttaagcg atttttattg
     4861 gtcggggtta tatttgcctt atcaatcgtt ttaagtggtt tattcggcgt tttagagggt
     4921 aataaacgtg tttcaagaag cattttatta ggggatatca ctcaaaagta tgaagcagca
     4981 tgtgataaaa agaaaaaaga gcaagcatta gcacaaaaaa tggaggaatt taccgcttgt
     5041 tatgaggaca tgaacaatat ttttgtggat caagagaaac gtttaacaga taaaaacatg
     5101 aaaaaactca ctcgttttta tcaaaactta ccagaaaaac agcaaaaaga ggtacaagaa
     5161 aaatatgagc aagtaaaaaa agacgtgcaa tattttaaag atacgcagac agaagaagct
     5221 tgttgtaact tatttagcga tacaatccct ttttcaacca gtgaacaaga acgaaaagaa
     5281 cggcaacaat cggtcacata cgaacgttat gaaacactgc ttcagcaagc aacaaacata
     5341 caaaatccaa cgaaaaaaga aacggcatta aattatctag aaagtgtcaa ggaatggttg
     5401 gatcagcaac aacaaaattg aatttgatta gcaatcatgt taaactgaac ctgcaaatga
     5461 tcaaacatta gatacacgaa agccccagag aggtcggatt ctctggggct ttttttcagg
     5521 ttgatgtcgc ctttattgat tttacttctt gtttcggtta ttcaaccaat aactgaataa
     5581 agagacacaa acttctacaa gaagggggca aatgaaccgt tcaaacatta gatacacctc
     5641 cttccagtcg caagactgtc ggataggcga caagttatta taccttacaa aataaaatct
     5701 gtgtggtgtt tttaagtatc ccttattttc gggttgttag ggcttgccct gaccgcctgt
     5761 aaggcgcttt aagaacaaga taaggttttt tacccaagac tgtcttaaaa cgacttagac
     5821 gagctatcag aggcttcccc cacctccgtt actgacttgt ttttagcaaa ggagccttta
     5881 ggcgactgcg cagtacaatg tgagagcata gcgatcacac ttttttagcg accgtaggga
     5941 gcaaggtttt gaattggcag ttttgaaaaa tgcgcgaacc tgttggtaga aaaaagaagt
     6001 ggtttttagg cgggaaattt tgtcaccctc ttttataatc tctttttaaa ccttttttta
     6061 aacctcttta ccgtcggctg tgtccttact ccttcaatgg atacagcgtt ttataaacta
     6121 cattttgtct gcttttaaac tacattttgt ctgcttttaa actacatttt gtctgctttt
     6181 aaactacatt ttgtctgctt ttaaactctt tttttgcact cacgtatgtt ataatatgca
     6241 ttatcacaga caaaacgttg tttataacgt ctgtatccat tgaaggagta aggaggaata
     6301 tct
//
