LOCUS       NZ_CP093946             6239 bp    DNA     circular CON 11-APR-2024
DEFINITION  Enterococcus faecium strain NY2032 plasmid pNY2032-5, complete
            sequence.
ACCESSION   NZ_CP093946
VERSION     NZ_CP093946.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26754680
            Assembly: GCF_022699225.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6239)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY2032
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6239)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAR-2022) State Key Laboratory of Pathogen and
            Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.
            20, Dongdajie, Fengtai, Beijing, Beijing 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022699225.1-RS_2024_04_10
            Annotation Date                   :: 04/10/2024 23:03:07
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,121
            CDSs (total)                      :: 3,030
            Genes (coding)                    :: 2,924
            CDSs (with protein)               :: 2,924
            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)              :: 106
            CDSs (without protein)            :: 106
            Pseudo Genes (ambiguous residues) :: 0 of 106
            Pseudo Genes (frameshifted)       :: 40 of 106
            Pseudo Genes (incomplete)         :: 63 of 106
            Pseudo Genes (internal stop)      :: 30 of 106
            Pseudo Genes (multiple problems)  :: 21 of 106
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093946.1.
            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..6239
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY2032"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY2032-5"
                     /geo_loc_name="China: BeiJing"
                     /lat_lon="39 N 116 E"
                     /collection_date="2018"
                     /collected_by="a public hospital"
     gene            join(6005..6239,1..44)
                     /locus_tag="MPL11_RS15480"
                     /old_locus_tag="MPL11_15480"
     CDS             join(6005..6239,1..44)
                     /locus_tag="MPL11_RS15480"
                     /old_locus_tag="MPL11_15480"
                     /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            51..740
                     /locus_tag="MPL11_RS15485"
                     /old_locus_tag="MPL11_15485"
     CDS             51..740
                     /locus_tag="MPL11_RS15485"
                     /old_locus_tag="MPL11_15485"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002369882.1"
                     /translation="MAFYLPYLLIFASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLPG
                     VIFTLSIVLSGLFGVLEGNKRISRSILLGDITQKYEAACDKKKKEQVLTQKMEEFTTCY
                     EEMNDIFVNQEKRLTDKNMEKLTRLYQNLPEKQQKEVQDNYERTKKDVQYFKDTQTEEA
                     CYNLFSDTIPFSTSEQERKERQQSVTYERYKALLQQATNIQNPTKKETALNYLKSVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            1584..2578
                     /locus_tag="MPL11_RS15490"
                     /old_locus_tag="MPL11_15490"
                     /pseudo=""
     CDS             1584..2578
                     /locus_tag="MPL11_RS15490"
                     /old_locus_tag="MPL11_15490"
                     /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="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /name="RepB family plasmid replication initiator protein"
     gene            2599..3132
                     /locus_tag="MPL11_RS15495"
                     /old_locus_tag="MPL11_15495"
     CDS             2599..3132
                     /locus_tag="MPL11_RS15495"
                     /old_locus_tag="MPL11_15495"
                     /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_002363576.1"
                     /translation="MQPQETFTIKELSDLFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLDNQRLLDKLHKHEQNNDKNAYIPNKNVVANKLLDQLREENEFLREQL
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENSSTTLSEATETMD
                     EQTKNWKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            3147..3317
                     /locus_tag="MPL11_RS15500"
                     /old_locus_tag="MPL11_15500"
     CDS             3147..3317
                     /locus_tag="MPL11_RS15500"
                     /old_locus_tag="MPL11_15500"
                     /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_032491833.1"
                     /translation="MTKKHLLFGSILLGILSFSPMLLSVANKGNKKGELKLNPNYYNSQ
                     NEEVFVEKLDK"
                     /name="hypothetical protein"
     gene            3787..4011
                     /locus_tag="MPL11_RS15505"
                     /old_locus_tag="MPL11_15505"
     CDS             3787..4011
                     /locus_tag="MPL11_RS15505"
                     /old_locus_tag="MPL11_15505"
                     /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            4031..4318
                     /locus_tag="MPL11_RS15510"
                     /old_locus_tag="MPL11_15510"
     CDS             4031..4318
                     /locus_tag="MPL11_RS15510"
                     /old_locus_tag="MPL11_15510"
                     /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            4769..5149
                     /locus_tag="MPL11_RS15515"
                     /old_locus_tag="MPL11_15515"
     CDS             4769..5149
                     /locus_tag="MPL11_RS15515"
                     /old_locus_tag="MPL11_15515"
                     /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_010782660.1"
                     /translation="MSEQNQYLASNHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVDPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5131..6045
                     /locus_tag="MPL11_RS15520"
                     /old_locus_tag="MPL11_15520"
     CDS             5131..6045
                     /locus_tag="MPL11_RS15520"
                     /old_locus_tag="MPL11_15520"
                     /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_010782659.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQIAIYTHTDKDHIHNHI
                     VINSVNLETGNKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYNQFCDSLKTFGIHCLNRGKNFTYELIHKKKKVRS
                     NKLGKDYEKETILHELDRRERAYNQQRTNELRRARASIRETAKEVRREQRTLTTEQPEI
                     RPTRRNHDQHVERGADYQQELSF"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     BGC             1..6239
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          1585..2297
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2299..2578
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.9e-144"
     Typing          5132..6042
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taatcatgac actgttagcc ttttggctgg tatggggaga ataaatagaa atggcattct
       61 atttacccta tctactcatt tttgccagta ttttaggaat tatttggctt agctataagg
      121 cttatcaaac aagatattca ttaaaaggct ctaaaattcg atttaagagg tttttattgc
      181 caggggttat atttacatta tcaatcgttt taagtggttt attcggcgtt ttagagggaa
      241 ataaacgtat ttcaagaagt attttattag gggatatcac tcaaaagtat gaagcagcat
      301 gtgataaaaa gaaaaaggag caagtgttaa cacaaaaaat ggaagagttt accacttgtt
      361 atgaggaaat gaacgatatt tttgtgaatc aagaaaaacg tttgacggat aaaaacatgg
      421 aaaaactcac tcgtctttat caaaacttgc cagaaaaaca gcaaaaagag gttcaagaca
      481 actatgagcg aaccaaaaaa gacgtgcaat attttaaaga tacgcagaca gaagaagctt
      541 gttataattt attcagtgat acaatccctt tttcaactag tgaacaggaa cgaaaagaac
      601 ggcaacaatc agttacctac gaacgttata aagcactgct tcagcaagca acgaacatac
      661 aaaatccaac gaaaaaagaa acggcattaa attatctaaa aagtgtcaag gaatggttag
      721 atcagcaaca gcaaaattga atttgatcgg caatcatgtt aaactaaaca tgcaaatgat
      781 caaacattag atacacgaaa gccccagaga ggtcggattc tctggggctt tttttcaggt
      841 tgatgtcgcc tttattgatt ttacttcttg tttcggttat tcaaccaata actgaataaa
      901 gagacacaaa cttctataag aagggggcaa atgaacaatt caaacattag atacacctcc
      961 ttccagtcgc aagactgtcg gataggcgac aagttattat atcttaaaaa attaaacttg
     1021 tgtggtgttt ttaagtatcg cttattttag ggttgttagg gcttgccctg accgcctgta
     1081 aggcgcttta aagctagata aggattttta tccaagactg tcttaaaacg gcttagataa
     1141 gcattcagaa ccgctcaaag gcctctttac caacatgttt ttagcaaagg agcctttagg
     1201 cgactgcgca gtacaatgtg agagcgtagc gatcacacct ttttggcgac cgtaggaagc
     1261 aaggttttgg attggcagtt ttgaaaaatg cgcgaacctg tttaaagaaa aaagaagtgg
     1321 tttttaggcg ggaaaattag cccccctctt tttatatctc tttttaaacc tctttttaaa
     1381 cctctttacc gtaagctgtg tccttactct accaatggat acagaatgtt atgaaggaca
     1441 ttttgtctgt ttatgaatga cattttgtct gtttatgaat gacattttgt ctgtttatga
     1501 aggacatttt gtctgtttga acgtcaaata tgaatgtctt gacatttaaa aaatgtcatt
     1561 cataattgga ttgaggtgat tatatggcta atgagattgt aaaataccac catgaattaa
     1621 atacaattcc tttaagaaaa tttacaccgg ttgaaatgaa tttgtttttt tccatcgtgt
     1681 ctagaatgcg tgaaaaaggg gataagacag ttcgttttac gtttgaccaa ctaaaagatt
     1741 taagtaacta caaagcaact gcaaatgtac gatttgtaga agatttaaaa gcaacttatg
     1801 aaaaaatctt atctttacgc tttggtcgta gaagtgagtc tgggctttct tacgatatgt
     1861 ttgtaatgtt tacagaattt aaaatcaacg gggacgtaga aaatccttac gtagatatac
     1921 gaatttacga aaaagcactg cctttgttaa ataatttaga cgagtgggta cgctattctt
     1981 tacaacaatt caacgagcta caaagtggct atgcaaagac tatgtttcgt ctgttaaagc
     2041 aatacagaac caaaggtttc gcatatttct ccaaagaaga ctttcttgaa ttattagata
     2101 ttcctaaaag ttataagcaa cctgatatag ataaacgagt tataaaacct atacgtcaag
     2161 aactaactgc aatcttcaaa ggactaacaa tcaaaaagaa atacggaaaa ggacggggaa
     2221 aacctgttat tggctatcaa tttacgttca aacctgagat caaaaaagca gacgacttta
     2281 acaaacatgc accaacctca aacctgagat caaaaaagca gacgacttta acaaacatgc
     2341 accaaccaaa gaagaccaaa ataaagcatt ggctttagct gataaacaaa aagaatacga
     2401 agaacccgct acaacaatta acgaaaaaat caaacagaag aaacgagaac ttgaactcct
     2461 ccaacaaatc aaacaactag aaaaagagaa aaaagctctt gaaaaacaaa cagagtccgc
     2521 actttcggaa aaagagaaaa aaagtttatt atctgattta gataatttat tccagtagca
     2581 acctaggagg caaccagtat gcaaccacaa gaaaccttta caataaagga attgtcagat
     2641 ctttttaaga tgagtaggca agcaatatcg aaacatatcc aaaaattaga ttcttccatg
     2701 atagctaaaa atgagcgtgg ttataaggtt gtattgcgtt ctggagtatt gcaacttgct
     2761 cgcaacttag acaatcaaag gttgctagat aagttgcata aacatgaaca aaacaacgat
     2821 aaaaatgctt atataccaaa caaaaacgtg gttgcaaaca agttgctaga tcagttgcgt
     2881 gaagaaaatg aatttttacg agaacaactt gccctcaaag agcaaaataa ttctcatata
     2941 caaaaactac tcgaccagca acaacaactc accctgcaag ccaaccaaca aatcgaaaaa
     3001 cttcaggagc aactgcagtt gacttatacg gaagagtctt cagagaatag ttcaacgact
     3061 ctttctgaag caacagaaac aatggacgaa caaacaaaga attggaaaaa atggtggcag
     3121 ctatggaaat gaagaaggaa atacttatga caaaaaaaca cttgctattc ggttctatcc
     3181 tactaggaat attaagcttt agcccaatgt tattatcagt ggccaacaaa ggaaataaaa
     3241 aaggggaact aaaactcaat cctaattact acaacagtca aaatgaggaa gtatttgtag
     3301 aaaaacttga taaataagaa aagactgctc gtacgagcag tctttctgaa agagattatc
     3361 ctattattaa ccttagaaaa gaataataaa tgaatatgag atatgtaaaa agcataacaa
     3421 acacaaacaa aaataacaag tatttaaaaa atgaccgatc aatattcaca aagaattaga
     3481 aagaaacaac cgcagaaaac caagccttaa aaagagcttt taacctagac caataaaaat
     3541 tcacaaaatc agcgcctgga tcccttggta caggcgttac ttggtagtat cgacattatg
     3601 tctactagct gtttaaataa ctgatcttat aattttattt aaacgattat gaattcaaaa
     3661 ctacttttta tgacgttaat cattgttata taataaaatg ttatataata aaatgttata
     3721 taataaaatt actaagatta tttaatataa caagcaattt taaaaaaacg aaaaggaaaa
     3781 acaatcatga aaaagaaagt attaaaacat tgtgttattc taggaatatt aggaacttgt
     3841 ctagctggca tcggtacagg aataaaagtt gatgcagcta cttactatgg aaatggtctt
     3901 tattgtaaca aagaaaaatg ttgggtagat tggaatcaag ctaaaggaga aattggaaaa
     3961 attattgtta atggttgggt taatcatggt ccatgggcac ctagaaggta gtggtaggga
     4021 ggttattata atggatttta ctaaagaaga aaaactttta aatgcaatta gtaaagtata
     4081 caatgaagca actatagatg actatcctga cttaaaagaa aagctctttc tttattctaa
     4141 agaaatcagt gagggaaaaa gtgttggtga agttagtatg aaattaagta gttttcttgg
     4201 aagatatatt ttaaaacata aatttggatt acctaaatct ttaatagaat tacaagaaat
     4261 tgttagtaag gaatctcaag tatatagagg atgggcttct attggtattt ggagttaatt
     4321 ctttggaata aaatgaaaat gggactgaag aatcaattct gattcatcag tcccataaat
     4381 tatagagccg aaaaattatc atatttatag atttattaat agtaaatggc ataagaatct
     4441 ttgaacaacg aaaaaaatgt agctctacct aattattgat ttgcaacaat ttcaccgaag
     4501 gtgaaacaag cgaaacttta caaaaagtgg ctagcatttg ctagtctttt ttgtattgtg
     4561 gagagtgggg ggggaggggg attcaagggg gagcttgcgc ccctttgaca agcggttatt
     4621 tgcaccaaat acgtaggtat ttggctagca aatatagagc ttgccaagcc ctttagtaag
     4681 ctttagtgag ctttacttat tgtacctttt taggtacaat ggtattgcga acgatacgtc
     4741 cgtaggacgt actgaaaggg tgggacttat gagcgaacaa aatcaatatt tggctagcaa
     4801 tcattctaaa aaatatacct atcgatccga gccaaaacaa atcagttttc gagtgagcga
     4861 atccgaattt gcaaagctga agcagtcagc tgaagctttg caaatgagtg tgccggcttt
     4921 cgtgaaagcc aaggcacaaa acgcgcgtct ggtgacaccg aaagtggcgc cagacattgc
     4981 tcaggcaatc gcgcgcgatt tagccaaagc tggcgggaat atcaatcaaa ttgccaagtg
     5041 gtgcaacaca caccaacacg acgttgatcc tggcgacgcc caacgcttat ccgaaaacct
     5101 aaaaatcatg caaaaggagc tacaaaagat atggcaacag ttaaagtaag ccgaaccact
     5161 tcttgtagcc gagcgatcaa ttacgccgaa ccacgagcaa ccgtcaaaac agggataaac
     5221 tgtgacattg attatgccaa aagcgaaatg aaacaaattc gcatgctgta tggaaaagac
     5281 gatcgtgtac aagcacactt attgatccag tcttttcgac caggagaaat taccgctgaa
     5341 aaagccaatc aactaggggc agagtatgcg aaaaaaatag cccctgacca ccaaatcgcg
     5401 atttacacac atacagacaa agaccatatt cataaccaca ttgtcattaa ctccgtcaat
     5461 ctggaaactg ggaacaaatt tcaagcccat ggtcaagcat ttttaaacaa atgttatgac
     5521 ctaaatgacg agatttgtct tgaacatgac ttaacaatca ctgaacgagg gaagaaaccc
     5581 gaaaaacgaa ccatgtctga aatcaaatta aaagaaaaaa atgaacctgt ttggaaagac
     5641 gaaattcggt ttgcgattga tcaaacaatg aaaaacaaaa aaactcgaac gtataaccaa
     5701 ttttgtgatt ctcttaaaac attcggcatt cattgcttga atcgtgggaa aaattttact
     5761 tacgaattga tccacaaaaa gaaaaaagta cgatccaaca aactaggaaa ggattacgaa
     5821 aaggagacga ttttacatga gctggacaga cgagaacgag cctacaatca acaacgaacc
     5881 aacgagctac gaagagctcg agctagcatt cgcgaaactg caaaagaagt acgaagagaa
     5941 caacgaactc ttacgactga acaaccggaa attagaccga ctcgaagaaa ccatgaccaa
     6001 cacgttgaaa gaggagcaga ctaccaacaa gaattatcgt tctaaaacgt tacaagacat
     6061 agaaaatgaa ataaagaaac aacgtgcttt tcttgcacct tataccaaag aaagaataca
     6121 aactacaatt gattcacaag tcaaaaaatt ccaccatgcg ctattaaacc agcgaaataa
     6181 agaacagaaa aaagtaatta tgcagcgatc aatggatatt cttgccccct tatgttgct
//
