LOCUS       NZ_CP093950             6174 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain NY11066 plasmid pNY11066-3, complete
            sequence.
ACCESSION   NZ_CP093950
VERSION     NZ_CP093950.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26754719
            Assembly: GCF_022699565.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6174)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY11066
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6174)
  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, Beijng 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v3.0
            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_022699565.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 06:19:43
            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)                     :: 3,181
            CDSs (total)                      :: 3,091
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 45 of 116
            Pseudo Genes (incomplete)         :: 65 of 116
            Pseudo Genes (internal stop)      :: 27 of 116
            Pseudo Genes (multiple problems)  :: 15 of 116
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093950.1.
            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..6174
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY11066"
                     /isolation_source="sanies"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY11066-3"
                     /geo_loc_name="China: Shandong"
                     /lat_lon="36 N 120 E"
                     /collection_date="2020"
                     /collected_by="a teaching hospital"
     gene            423..1367
                     /locus_tag="MPL63_RS15705"
                     /old_locus_tag="MPL63_15705"
     CDS             423..1367
                     /locus_tag="MPL63_RS15705"
                     /old_locus_tag="MPL63_15705"
                     /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_002303559.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVEDLKATYEKILSLRFGRRSESGLSYDMFVMFTEFKINGD
                     VENPYVDIRIYEKALPLLNNLDEWVRYSLQQFNELQSGYAKTMFRLLKQYRTKGFAYFS
                     KEDFLELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQIKQ
                     LEKEKKALEKQTESALSEKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            1388..1921
                     /locus_tag="MPL63_RS15710"
                     /old_locus_tag="MPL63_15710"
     CDS             1388..1921
                     /locus_tag="MPL63_RS15710"
                     /old_locus_tag="MPL63_15710"
                     /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            1936..2106
                     /locus_tag="MPL63_RS15715"
                     /old_locus_tag="MPL63_15715"
     CDS             1936..2106
                     /locus_tag="MPL63_RS15715"
                     /old_locus_tag="MPL63_15715"
                     /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            2561..2785
                     /locus_tag="MPL63_RS15720"
                     /old_locus_tag="MPL63_15720"
     CDS             2561..2785
                     /locus_tag="MPL63_RS15720"
                     /old_locus_tag="MPL63_15720"
                     /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            2805..3092
                     /locus_tag="MPL63_RS15725"
                     /old_locus_tag="MPL63_15725"
     CDS             2805..3092
                     /locus_tag="MPL63_RS15725"
                     /old_locus_tag="MPL63_15725"
                     /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            3543..3923
                     /locus_tag="MPL63_RS15730"
                     /old_locus_tag="MPL63_15730"
     CDS             3543..3923
                     /locus_tag="MPL63_RS15730"
                     /old_locus_tag="MPL63_15730"
                     /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            3905..4819
                     /locus_tag="MPL63_RS15735"
                     /old_locus_tag="MPL63_15735"
     CDS             3905..4819
                     /locus_tag="MPL63_RS15735"
                     /old_locus_tag="MPL63_15735"
                     /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"
     gene            5064..5753
                     /locus_tag="MPL63_RS15740"
                     /old_locus_tag="MPL63_15740"
     CDS             5064..5753
                     /locus_tag="MPL63_RS15740"
                     /old_locus_tag="MPL63_15740"
                     /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"
     BGC             1..6174
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          424..1367
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3906..4816
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cctctttacc aacatgtttt tagcaaagga gcctttaggc gactgcgcag tacaatgtga
       61 gagcgtagcg atcacacctt tttggcgacc gtaggaagca aggttttgga ttggcagttt
      121 tgaaaaatgc gcgaacctgt ttaaagaaaa aagaagtggt ttttaggcgg gaaaattagc
      181 ccccctcttt ttatatctct ttttaaacct ctttttaaac ctctttaccg taagctgtgt
      241 ccttactcta ccaatggata cagaatgtta tgaaggacat tttgtctgtt tatgaatgac
      301 attttgtctg tttatgaatg acattttgtc tgtttatgaa ggacattttg tctgtttgaa
      361 cgtcaaatat gaatgtcttg acatttaaaa aatgtcattc ataattggat tgaggtgatt
      421 atatggctaa tgagattgta aaataccacc atgaattaaa tacaattcct ttaagaaaat
      481 ttacaccggt tgaaatgaat ttgttttttt ccatcgtgtc tagaatgcgt gaaaaagggg
      541 ataagacagt tcgttttacg tttgaccaac taaaagattt aagtaactac aaagcaactg
      601 caaatgtacg atttgtagaa gatttaaaag caacttatga aaaaatctta tctttacgct
      661 ttggtcgtag aagtgagtct gggctttctt acgatatgtt tgtaatgttt acagaattta
      721 aaatcaacgg ggacgtagaa aatccttacg tagatatacg aatttacgaa aaagcactgc
      781 ctttgttaaa taatttagac gagtgggtac gctattcttt acaacaattc aacgagctac
      841 aaagtggcta tgcaaagact atgtttcgtc tgttaaagca atacagaacc aaaggtttcg
      901 catatttctc caaagaagac tttcttgaat tattagatat tcctaaaagt tataagcaac
      961 ctgatataga taaacgagtt ataaaaccta tacgtcaaga actaactgca atcttcaaag
     1021 gactaacaat caaaaagaaa tacggaaaag gacggggaaa acctgttatt ggctatcaat
     1081 ttacgttcaa acctgagatc aaaaaagcag acgactttaa caaacatgca ccaaccaaag
     1141 aagaccaaaa taaagcattg gctttagctg ataaacaaaa agaatacgaa gaacccgcta
     1201 caacaattaa cgaaaaaatc aaacagaaga aacgagaact tgaactcctc caacaaatca
     1261 aacaactaga aaaagagaaa aaagctcttg aaaaacaaac agagtccgca ctttcggaaa
     1321 aagagaaaaa aagtttatta tctgatttag ataatttatt ccagtagcaa cctaggaggc
     1381 aaccagtatg caaccacaag aaacctttac aataaaggaa ttgtcagatc tttttaagat
     1441 gagtaggcaa gcaatatcga aacatatcca aaaattagat tcttccatga tagctaaaaa
     1501 tgagcgtggt tataaggttg tattgcgttc tggagtattg caacttgctc gcaacttaga
     1561 caatcaaagg ttgctagata agttgcataa acatgaacaa aacaacgata aaaatgctta
     1621 tataccaaac aaaaacgtgg ttgcaaacaa gttgctagat cagttgcgtg aagaaaatga
     1681 atttttacga gaacaacttg ccctcaaaga gcaaaataat tctcatatac aaaaactact
     1741 cgaccagcaa caacaactca ccctgcaagc caaccaacaa atcgaaaaac ttcaggagca
     1801 actgcagttg acttatacgg aagagtcttc agagaatagt tcaacgactc tttctgaagc
     1861 aacagaaaca atggacgaac aaacaaagaa ttggaaaaaa tggtggcagc tatggaaatg
     1921 aagaaggaaa tacttatgac aaaaaaacac ttgctattcg gttctatcct actaggaata
     1981 ttaagcttta gcccaatgtt attatcagtg gccaacaaag gaaataaaaa aggggaacta
     2041 aaactcaatc ctaattacta caacagtcaa aatgaggaag tatttgtaga aaaacttgat
     2101 aaataagaaa agactgctcg tacgagcagt ctttctgaaa gagattatcc tattattaac
     2161 cttagaaaag aataataaat gaatatgaga tatgtaaaaa gcataacaaa cacaaacaaa
     2221 aataacaagt atttaaaaaa tgaccgatca atattcacaa agaattagaa agaaacaacc
     2281 gcagaaaacc aagccttaaa aagagctttt aacctagacc aataaaaatt cacaaaatca
     2341 gcgcctggat cccttggtac aggcgttact tggtagtatg tacattatgt ctactagctg
     2401 tttaaataac tgatcttata attttattta aacgattatg aattcaaaac tactttttat
     2461 gacgttaatc attgttatat aataaaatgt tatataataa aattactaag attatttaat
     2521 ataacaagca attttaaaaa aacgaaaagg aaaaacaatc atgaaaaaga aagtattaaa
     2581 acattgtgtt attctaggaa tattaggaac ttgtctagct ggcatcggta caggaataaa
     2641 agttgatgca gctacttact atggaaatgg tctttattgt aacaaagaaa aatgttgggt
     2701 agattggaat caagctaaag gagaaattgg aaaaattatt gttaatggtt gggttaatca
     2761 tggtccatgg gcacctagaa ggtagtggta gggaggttat tataatggat tttactaaag
     2821 aagaaaaact tttaaatgca attagtaaag tatacaatga agcaactata gatgactatc
     2881 ctgacttaaa agaaaagctc tttctttatt ctaaagaaat cagtgaggga aaaagtgttg
     2941 gtgaagttag tatgaaatta agtagttttc ttggaagata tattttaaaa cataaatttg
     3001 gattacctaa atctttaata gaattacaag aaattgttag taaggaatct caagtatata
     3061 gaggatgggc ttctattggt atttggagtt aattctttgg aataaaatga aaatgggact
     3121 gaagaatcaa ttctgattca tcagtcccat aaattataga gccgaaaaat tatcatattt
     3181 atagatttat taatagtaaa tggcataaga atctttgaac aacgaaaaaa atgtagctct
     3241 acctaattat tgatttgcaa caatttcacc gaaggtgaaa caagcgaaac tttacaaaaa
     3301 gtggctagca tttgctagcc ttttttgtat tgtggagcgt ggtttttgag ggggattcaa
     3361 gggggagctt gcgccccttt gacaagcggt tatttgcacc aaatacgtag gtatttggct
     3421 agcaaatata gagcttgcca agccctttag taagctttag tgagctttac ttattgtacc
     3481 tttttaggta caatggtatt gcgaacgata cgtccgtagg acgtactgaa agggtgggac
     3541 ttatgagcga acaaaatcaa tatttggcta gcaatcattc taaaaaatat acctatcgat
     3601 ccgagccaaa acaaatcagt tttcgagtga gcgaatccga atttgcaaag ctgaagcagt
     3661 cagctgaagc tttgcaaatg agtgtgccgg ctttcgtgaa agccaaggca caaaacgcgc
     3721 gtctggtgac accgaaagtg gcgccagaca ttgctcaggc aatcgcgcgc gatttagcca
     3781 aagctggcgg gaatatcaat caaattgcca agtggtgcaa cacacaccaa cacgacgttg
     3841 atcctggcga cgcccaacgc ttatccgaaa acctaaaaat catgcaaaag gagctacaaa
     3901 agatatggca acagttaaag taagccgaac cacttcttgt agccgagcga tcaattacgc
     3961 cgaaccacga gcaaccgtca aaacagggat aaactgtgac attgattatg ccaaaagcga
     4021 aatgaaacaa attcgcatgc tgtatggaaa agacgatcgt gtacaagcac acttattgat
     4081 ccagtctttt cgaccaggag aaattaccgc tgaaaaagcc aatcaactag gggcagagta
     4141 tgcgaaaaaa atagcccctg accaccaaat cgcgatttac acacatacag acaaagacca
     4201 tattcataac cacattgtca ttaactccgt caatctggaa actgggaaca aatttcaagc
     4261 ccatggtcaa gcatttttaa acaaatgtta tgacctaaat gacgagattt gtcttgaaca
     4321 tgacttaaca atcactgaac gagggaagaa acccgaaaaa cgaaccatgt ctgaaatcaa
     4381 attaaaagaa aaaaatgaac ctgtttggaa agacgaaatt cggtttgcga ttgatcaaac
     4441 aatgaaaaac aaaaaaactc gaacgtataa ccaattttgt gattctctta aaacattcgg
     4501 cattcattgc ttgaatcgtg ggaaaaattt tacttacgaa ttgatccaca aaaagaaaaa
     4561 agtacgatcc aacaaactag gaaaggatta cgaaaaggag acgattttac atgagctgga
     4621 cagacgagaa cgagcctaca atcaacaacg aaccaacgag ctacgaagag ctcgagctag
     4681 cattcgcgaa actgcaaaag aagtacgaag agaacaacga actcttacga ctgaacaacc
     4741 ggaaattaga ccgactcgaa gaaaccatga ccaacacgtt gaaagaggag cagactacca
     4801 acaagaatta tcgttctaaa acgttacaag acatagaaaa tgaaataaag aaacaacgtg
     4861 cttttcttgc accttatacc aaagaaagaa tacaaactac aattgattca caagtcaaaa
     4921 aattccacca tgcgctatta aaccagcgaa ataaagaaca gaaaaaagta attatgcagc
     4981 gatcaatgga tattcttgcc cccttatgtt gcttaatcat gacactgtta gccttttggc
     5041 tggtatgggg agaataaata gaaatggcat tctatttacc ctatctactc atttttgcca
     5101 gtattttagg aattatttgg cttagctata aggcttatca aacaagatat tcattaaaag
     5161 gctctaaaat tcgatttaag aggtttttat tgccaggggt tatatttaca ttatcaatcg
     5221 ttttaagtgg tttattcggc gttttagagg gaaataaacg tatttcaaga agtattttat
     5281 taggggatat cactcaaaag tatgaagcag catgtgataa aaagaaaaag gagcaagtgt
     5341 taacacaaaa aatggaagag tttaccactt gttatgagga aatgaacgat atttttgtga
     5401 atcaagaaaa acgtttgacg gataaaaaca tggaaaaact cactcgtctt tatcaaaact
     5461 tgccagaaaa acagcaaaaa gaggttcaag acaactatga gcgaaccaaa aaagacgtgc
     5521 aatattttaa agatacgcag acagaagaag cttgttataa tttattcagt gatacaatcc
     5581 ctttttcaac tagtgaacag gaacgaaaag aacggcaaca atcagttacc tacgaacgtt
     5641 ataaagcact gcttcagcaa gcaacgaaca tacaaaatcc aacgaaaaaa gaaacggcat
     5701 taaattatct aaaaagtgtc aaggaatggt tagatcagca acagcaaaat tgaatttgat
     5761 cggcaatcat gttaaactaa acatgcaaat gatcaaacat tagatacacg aaagccccag
     5821 agaggtcgga ttctctgggg ctttttttca ggttgatgtc gcctttattg attttacttc
     5881 ttgtttcggt tattcaacca ataactgaat aaagagacac aaacttctat aagaaggggg
     5941 caaatgaaca attcaaacat tagatacacc tccttccagt cgcaagactg tcggataggc
     6001 gacaagttat tatatcttaa aaaattaaac ttgtgtggtg tttttaagta tcgcttattt
     6061 tagggttgtt agggcttgcc ctgaccgcct gtaaggcgct ttaaagctag ataaggattt
     6121 ttatccaaga ctgtcttaaa acggcttaga taagcattca gaaccgctca aagg
//
