LOCUS       NZ_AP028419             5851 bp    DNA     circular CON 01-NOV-2023
DEFINITION  Enterococcus faecium strain 8419 plasmid pSU8419_4, complete
            sequence.
ACCESSION   NZ_AP028419
VERSION     NZ_AP028419.1
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  JOURNAL   Unpublished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 5851)
  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
            AP028419.1.
            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..5851
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="8419"
                     /isolation_source="Necrosectomy"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pSU8419_4"
                     /geo_loc_name="Japan:Nagano, Matsumoto"
                     /collection_date="2022-08-31"
     gene            1..978
                     /locus_tag="R9B63_RS15290"
                     /old_locus_tag="SUGS_500010"
     CDS             1..978
                     /locus_tag="R9B63_RS15290"
                     /old_locus_tag="SUGS_500010"
                     /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            988..1485
                     /locus_tag="R9B63_RS15295"
                     /old_locus_tag="SUGS_500020"
     CDS             988..1485
                     /locus_tag="R9B63_RS15295"
                     /old_locus_tag="SUGS_500020"
                     /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            1861..2142
                     /locus_tag="R9B63_RS15300"
                     /old_locus_tag="SUGS_500030"
     CDS             1861..2142
                     /locus_tag="R9B63_RS15300"
                     /old_locus_tag="SUGS_500030"
                     /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            2144..2560
                     /locus_tag="R9B63_RS15305"
                     /old_locus_tag="SUGS_500040"
     CDS             2144..2560
                     /locus_tag="R9B63_RS15305"
                     /old_locus_tag="SUGS_500040"
                     /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            3169..4323
                     /locus_tag="R9B63_RS15310"
                     /old_locus_tag="SUGS_500050"
     CDS             3169..4323
                     /locus_tag="R9B63_RS15310"
                     /old_locus_tag="SUGS_500050"
                     /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            4296..4739
                     /locus_tag="R9B63_RS15315"
                     /old_locus_tag="SUGS_500060"
     CDS             4296..4739
                     /locus_tag="R9B63_RS15315"
                     /old_locus_tag="SUGS_500060"
                     /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            4996..>5186
                     /locus_tag="R9B63_RS15320"
                     /pseudo=""
     CDS             4996..>5186
                     /locus_tag="R9B63_RS15320"
                     /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          2..978
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaaatg aaattgtgaa ataccaccat gaattaaata cgattccttt acgcaaattt
       61 acgtcagtag aaatgaattt attcttctct atagtatcta gaatgcgtga cgtaggcgat
      121 aaaaaagtac aatttacatt cgaacaatta aaagatttaa gcaattataa agcaactgca
      181 aatgttcgat tcatagatga tttagaaaca acgtatgaca aattaatgga tttacgtttt
      241 ggtagaagaa gtgctgacgg tttgcaacgt gaacgatttg ttttatttaa tcaatttaaa
      301 atcgatggaa aagctgatat tccttttgct gaaatacaag tccatgagaa agccttaccc
      361 ttacttaata atcttgaaga atgggttcga tattctctcc aacaattcaa tgaattagaa
      421 agcagttatt ccaaaaccat gtttagatta ttaaaacaat acagaaccaa aggaattgcc
      481 tatttttcaa aagaagactt tcatgaatta cttgatatcc ctaaaagtta tagagaaagt
      541 gatataaata aaaaaattat aaagcctatt cgccaagaac taaccgcaat cttcaaaggt
      601 ctgacaatca aaaagaaata cggaaaagga agaggaaaac ctgtcattgg ctatcaattc
      661 acgtttaaac ctgaaataaa aaaagcagac gactttaata aacacgcacc aacaaaagaa
      721 gaacaaaata aagctttaga actagttaat caacaaattt actctgaaaa agaccccact
      781 tcattacaag aaaaaatcaa agaacagaaa cgaaaattag aacttttaca acaattagaa
      841 gagctagaaa gaaaacaaaa taatctgaat aaagaaaata aggagattaa cgaacaaata
      901 ccagataaca attccgatat tcccccagaa ttaaaaaaag gcttactaga taatcttcaa
      961 aacttattta aagaataagg ggtttttatg acagataaaa ctatcaaaga attagcagat
     1021 attctaggtg tttcaaaaga taaagtgaag tatcaactga ggaaattacc tagtaatttt
     1081 acctacaaaa aaggaaatat tatctacctg aaaaaagaag cagtaacaac aattacaaag
     1141 gttttatcag gtaatgagcc gggtaactta cctagtgaat tacctgattc attacctacc
     1201 gattacctac tcaaggagat tgaaactaag aataatcata ttgaagaaaa agataggcaa
     1261 attgaaaaac ttcaactagc tttagaaaca caacaaaaat tactcgacca gcaacaacaa
     1321 ctcaccctgc aagccaacca acaaatcgag aaactgcagg aacaactaca gttgacttat
     1381 acggaagaat cttcggaaaa taaatcaacg actctttctg aagaaacaga atcgatagaa
     1441 aaacaatcaa agacggagaa aaaatggtgg caattctggc aataaaacca gcaatttaaa
     1501 ttaataaaaa ttgctggttt tattcttctt tttgcttttg cgagcagagc aacatgggcc
     1561 catgttgcga tattttggtg gcgccccaat ccccgttttt tcgttgaatc ttactcggac
     1621 tgcactcgtt ttacagctga tttttctgaa ttttgaaaga gcataaggaa acgtggtatc
     1681 actttcttac gaaaggtgct agataagctg tgcctatcac gtttctcaga aaaaaatttg
     1741 ctatcacttt tttgccattg tggctaggct atgtatagtg ttttggcgaa aaatagctat
     1801 acaaatacta tatttgtatg atatacataa attatatact gatacgaaag gaaaatttcc
     1861 atggacattt tagttcgaaa tatcaatccc aaaattatta caagaataga taaacgttgt
     1921 caggaactaa caaccaaaac gggcaaaaaa tggagtcgaa atcaatacct aaaaatttta
     1981 atcgaaaacg attttgacca cgaacttatg aattacaaaa aagatcaatt cgatttatta
     2041 ttcgaaaaat ttattgccat tcaagcagaa aatacgaaca tactaaatga ctatgttcac
     2101 acaaacaacc aactcattga aacacttatc ggaggaatat aacatgagaa aaacttctgt
     2161 tcaaaaacac gtaacccttt atcccagtca cgttgacgtt ttagattcca tcatcgaaaa
     2221 aaatccagac gtcaacaatt attcagaagc cattcgcttt ttatgtatga gttatgaacc
     2281 tgctaccaat acaaccacaa ccagtaacca agcaaaactc aatgccatgg gaaaagaaat
     2341 ttctatcatg acagaaatca tggcagaatt tgctgattta tatctaaaag atactggtgt
     2401 tcttatcggt acaaattcta aagtatatca agaagtgaaa gaaaaaattg aaaatcaact
     2461 caatccttcc cgacgaaatc aacccaaaaa tcgtcaaaaa gaaaccaatc aaacctttac
     2521 ttctggaaat tttgacccaa caaactttct aaaaagataa aaaaagaaac cgaaaaataa
     2581 aaaaattcct cgatttcttt ttagggatcg gtcttccagc aagatttgca agttggtacc
     2641 aacttgcgaa aaaaaaaaag aaaaatccgc ttctgcgaat tcttcttttt tcattttggg
     2701 gcgctgccct aatccctaag tcccggttat tcaatagcat ggaaactcaa agaataagac
     2761 gttccctgga ataaaaaaaa ggctgctcgt tcgagcagtc catacatagg aaaatgaaaa
     2821 aacgacgtcc cttactgaga aacgctatta aacttttaac aaatcctcta aaaaataaca
     2881 agtctttaaa aagtgaccgg taaaaatgca caaagaacta aaaaagagaa attgcatcaa
     2941 atcaagcatt agaagctagt aactagctag accaattgaa aatcacaaag tgagcgcctg
     3001 tatctattgc tacaggcgct acttggcata gtcgacatta tgttaactaa cgctataaat
     3061 aacgattatg ttcccaaaac aatattttat gaactataac aaaaatttgt tatcgcatat
     3121 tgtatatttt aattataggt gtataccact taaatttaac acaaaggcgt gattattttg
     3181 aaacccaaaa agaaaattta tctaggtctc ctcttttcct tgatgattgg aatttttagt
     3241 ataggaatta caaataccta tgcttcagaa aattctaatt tcaatatcaa ctcccaacca
     3301 attgaagaac aagcaattaa ttttgcgaaa actgattttg aacactccat aacttcaatt
     3361 cttttaatgg aaaataacac cgaaactgat attaactata ctcttggttc gccatttaaa
     3421 atgctcgatg gagaaaatac ggcaaatagt tctattttct ttccagtatt ttcagacgct
     3481 gataatacga ttaaatatat ttataccgtc aaaaaaaata caaatggaga atattcagga
     3541 agtatttcac aatttttagc aaaagaactt caaaatctag tagatagtaa tataacagat
     3601 acaaccttat tttttcaaga taatagcatt tattattccg ataatggaca aattaaacta
     3661 ctttggaaat cacctttaag tacagaaaaa aatggtgttt cttcctttac agaaaaaaat
     3721 gatcttatat ccgtaaatat aaaaaataaa attaaaaatt tctctaaaaa acaaaatttt
     3781 cctgcggtta aacgtgtaaa aagtgtctcc tccggagata actttattat gattaattgg
     3841 cgtatagcag aaacccaaac aagttttccg tggtgtgctg cttacgtaga agctgctatc
     3901 ttatgtaaca aaacagatgt acatgctact tcagctagag ccattatgca ttatacctat
     3961 cctaatttaa acaacagtca aattgaatca aaaagtctta atcaagatca aataataaaa
     4021 tatgcaaatt actgtggtgt ttatcctaaa aaagtagcac gaatactaaa cctttcagag
     4081 gtccaaacac aactaagaaa aggaaatgcc atttatatgg gaactgctgg ttatggaaat
     4141 tatagtaaca gccgtcatgc acttgcatta tttgggtggg tcaatcaagg tggttatcaa
     4201 acttactatg tgtggaatcc ttggtataac tacccaactg taataagtgc aaatgcagga
     4261 ccagttacaa ttcctgtacc tggaggtggt tttacttggg acaataccat tacaaattgg
     4321 taaataaacc cattgcttta gttatgggtc tagtgttagt tcttttctta actagttgtt
     4381 caaaaaaaca agaaatacaa aagactgatc tgattccttt tctaggaact tggcaaacta
     4441 aagatcattc agaacgtcta gtaatcacta atttaaatac ttcaaaaaat atagaacaat
     4501 ataccatctt agtaaaagag aacaatcata aaattcaaat cattgataaa aatttaaata
     4561 taaatgaaca agttttcatt tacaaagcaa caaataattt actaacactg cgctctaata
     4621 aaaaacaatt agattacact tttagtttgg attctccaaa aaagctcgta tttattttga
     4681 caacgaatga tgggacagaa gggacagcta aaccaattga attttttaaa gctgattgat
     4741 gaatagttgt ttgatattac aaaacaataa tttcaccgaa ggtgaaacaa gcgaaacttt
     4801 acaaaaagtg gctagcattt gctagccttt tttgtattgt ggagcgtggg ttttgagggg
     4861 gattcaaggg ggagcttgcg cccctttgaa aagcggttat ttgcaccaaa tacgtaggta
     4921 tttggctagc aaatatagag cttgccaagc ccttttggtg agctttactc attgtgcctt
     4981 tttaggtaca atggtattgc gaacgatacg tccgtaggac gtactgaaag ggtgggactt
     5041 atgagcgaac aaaatcaaaa tttggctagc gatcattcta aaaaatatac ctatcgatcc
     5101 aagccaaaac aaatcagttt tcgagtgagc gaatctgaat ttgcaaagct gaagctttgc
     5161 aaatgagtgt gccggcttcc gtaaaaatac atatggctat aatttgcgtt ttaaggcgtt
     5221 ttaaacgttc tggtatataa tttataccaa aacaacttta aaacgcctta gatctaattt
     5281 tagaggtctt atagaacatt ttagggttgt tagggcttgc cctgaccgcc tgtaaggcgc
     5341 tttgagaaca agataagggt tttatactaa gactgtctta aaacggctta aacaaacgct
     5401 cagaactttt caaaggagtt ctttatgaac tgtttttaag caaaggagcc tttaggcgac
     5461 tgcgcagtat aatgtgagag cgtagcgatc acacattttt agtgaccgta gggagcgagt
     5521 ttcccagttt agaaaaattc gcgaacttgt ttgaggaaaa aagcaggagt tttttaggcg
     5581 ggaaattttg cctcctcttt tataatctct ttttaaacct ctttttaaac ctctttaccg
     5641 tcggctgtat gcttactctc ccaaggtgtg cagaatcttt tgggggtctt tttgtctgtt
     5701 tttaggggtc tttttgtctg tttttagggg tctttttgtc tgtttttggg ggtctttttg
     5761 tctgttttta ggggtcttta attaggggct tgacccctat tagaaagctc tttataattt
     5821 tgttaagtag ttaatcttga aggaggattt t
//
