LOCUS       NZ_CP093951             6303 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain NY11066 plasmid pNY11066-4, complete
            sequence.
ACCESSION   NZ_CP093951
VERSION     NZ_CP093951.1
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 6303)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY11066
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6303)
  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
            CP093951.1.
            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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY11066"
                     /isolation_source="sanies"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY11066-4"
                     /geo_loc_name="China: Shandong"
                     /lat_lon="36 N 120 E"
                     /collection_date="2020"
                     /collected_by="a teaching hospital"
     gene            442..1392
                     /locus_tag="MPL63_RS15745"
                     /old_locus_tag="MPL63_15745"
     CDS             442..1392
                     /locus_tag="MPL63_RS15745"
                     /old_locus_tag="MPL63_15745"
                     /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            1413..1946
                     /locus_tag="MPL63_RS15750"
                     /old_locus_tag="MPL63_15750"
     CDS             1413..1946
                     /locus_tag="MPL63_RS15750"
                     /old_locus_tag="MPL63_15750"
                     /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            1962..2132
                     /locus_tag="MPL63_RS15755"
                     /old_locus_tag="MPL63_15755"
     CDS             1962..2132
                     /locus_tag="MPL63_RS15755"
                     /old_locus_tag="MPL63_15755"
                     /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            2582..3115
                     /locus_tag="MPL63_RS15760"
                     /old_locus_tag="MPL63_15760"
     CDS             2582..3115
                     /locus_tag="MPL63_RS15760"
                     /old_locus_tag="MPL63_15760"
                     /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            3127..3330
                     /locus_tag="MPL63_RS15765"
                     /old_locus_tag="MPL63_15765"
     CDS             3127..3330
                     /locus_tag="MPL63_RS15765"
                     /old_locus_tag="MPL63_15765"
                     /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            3652..4032
                     /locus_tag="MPL63_RS15770"
                     /old_locus_tag="MPL63_15770"
     CDS             3652..4032
                     /locus_tag="MPL63_RS15770"
                     /old_locus_tag="MPL63_15770"
                     /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            4014..4928
                     /locus_tag="MPL63_RS15775"
                     /old_locus_tag="MPL63_15775"
     CDS             4014..4928
                     /locus_tag="MPL63_RS15775"
                     /old_locus_tag="MPL63_15775"
                     /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            5173..5862
                     /locus_tag="MPL63_RS15780"
                     /old_locus_tag="MPL63_15780"
     CDS             5173..5862
                     /locus_tag="MPL63_RS15780"
                     /old_locus_tag="MPL63_15780"
                     /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          444..1392
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4015..4925
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttagcaaagg agcctttagg cgactgcgca gtacaatgtg agagcatagc gatcacactt
       61 ttttagcgac cgtagggagc aaggttttga attggcagtt ttgaaaaatg cgcgaacctg
      121 ttggtagaaa aaagaagtgg tttttaggcg ggaaattttg tcaccctctt ttataatctc
      181 tttttaaacc tttttttaaa cctctttacc gtcggctgtg tccttactcc ttcaatggat
      241 acagcgtttt ataaactaca ttttgtctgc ttttaaacta cattttgtct gcttttaaac
      301 tacattttgt ctgcttttaa actacatttt gtctgctttt aaactctttt tttgcactca
      361 cgtatgttat aatatgcatt atcacagaca aaacgttgtt tataacgtct gtatccattg
      421 aaggagtaag gaggaatatc tttggcaaat gaaatcgtga aataccatca tgaattaaat
      481 accattccgt tgcggaaatt tacaccagtt gaaatgaatc tatttttctc tattgtgtct
      541 agaatgcgcg aaaaaggcga taaaacagtc cgtcttactt ttgaccaact aaaagattta
      601 agtaattata aagcaactgc taataatcgt ttcattaatg atttagaaat gacttatgat
      661 aaattaatgg atttacgttt tggtaaaaga agtgctaatg ggctcgatat agatagattc
      721 gttatgttta gtgagtttaa aatacgtgga actgctaaag atccatatgt agacatacaa
      781 gtttacgaaa aagctttacc tttactaaac aatttagatg agtgggttcg ctattcactc
      841 caacaattta acgaattaca aagtagctat gcaaagacta tgtttcgatt actaaaacaa
      901 tatcgaacta aaggttttgc ttatttttct aaagaggatt ttcatgaact attagatatt
      961 ccaaaaagtt actggaacaa ccaagcaaac gttgataatc gtgttataaa gcctatacga
     1021 caggaattaa ccgcaatctt caaaggatta tcaatcaaaa agaaatacgg aaaagggcga
     1081 ggaaaacctg tcgttggcta tcaatttacg tttaaaccag aaatcaaaaa agcagatgat
     1141 tttaataaac atgcaccaac caaagaagaa caaaataaag cattggcttt agctgataaa
     1201 caaaaagaat acgaagaacc tgctacaaca attaacgaaa aaatcaaaca gaagaaacga
     1261 gaacttgaac tcctccaaca aatcaaacaa ctagaaaaag agaaagaagc tcttgaaaaa
     1321 caaacagagt ccgcactttc gaaaaaagag aaaaaaagtt tattatctga tttagataat
     1381 ttattccagt agcaacctag gaggcaacca gtatgcaacc acaagaaacc tttacaataa
     1441 aggaattgtc agaacttttt aagatgagta ggcaagcaat atcgaaacat atccaaaaat
     1501 tagattcttc catgatagct aaaaatgagc gtggttataa ggttgtattg cgttctggag
     1561 tattgcaact tgctcgcaac ttaggcaacc aaatgttgct agataggttg cacgagtacg
     1621 aacaagacaa cgataaaaat gttaatatac caagcaaaaa cgtggttaca aacaagttgc
     1681 tagatcagtt gcgtgaagaa aatgaatttt tacgagaaca acttgccctc agagagcaaa
     1741 ataattctca tatacaaaaa ctactcgacc agcaacaaca actcacccta caagccaaca
     1801 aacaaatcga aaaactgcaa gaaaaactac agttgactta tacagaagaa gctccagaga
     1861 atgactcaac gactctttct gaagcaacag aaacaataga caaacaaatt gatactgaaa
     1921 aaaaatggtg gcaactttgg aaataactgg agggaacatt catgacaaga aaaaatcttc
     1981 tattcggttc tattttacta ggaattctag gattcagtcc gatgttattg tcagtgatca
     2041 ataaagggaa taaacatggt gaattgaaat tgaatccaaa ttattacaac agtcctaacg
     2101 aagaattgtt tgtaaaagaa acagataaat aataaaaaag actgctcttt cgagcagcca
     2161 gttaaaaaat aatgagtgtt tattcttgaa aaagcaacgc gcttatgaag cgctaccaaa
     2221 aatttatcat attttattaa aaataacaac ccagtaaaaa atgactggta aaaattcaca
     2281 aagaaacgga aagaagcaac cgcagaaaat caagcttaaa aagagctttt gacctagacc
     2341 aatcgaaaat cacaaagtga gcctctgtat cggttgatac aagggctact tggcatagtg
     2401 tacattatgt caacaagaat ttaatataac atattttcct aatgcattct aactatacca
     2461 cattatcaaa aatataaatt atctttacta aataaaatat tgacaagcct ataccttttg
     2521 ttttatgatt ttcacaaaga aaacgttttc tatatatttt tctgtatcag gaggaaattc
     2581 tatgaaaaaa tttactttag gggtagcttt gttaactatt ggggcagttg ttttaccgtc
     2641 aactactata gtttatgctt cagaaaattc ccaagtggta tcattaaacg aaaacaatgc
     2701 tactgaaaat gtagttattg agtacactga agatggtatg gtcgtaacta aatatgagga
     2761 tggttatagt gcggaagatt ttgcaaattc ttcagatatc atgacaagag ctgcagttgc
     2821 aagatggggc aaaaaggaat atacaaatat tgctgtaacc actggagtag ctgctaatgc
     2881 tattaatgct gccttttggg caggagggaa agctagcact tctatgtttg gtatcccagg
     2941 ttgggcaatt ggtgctttgt taacaggtgc aagttggact aaaaaaggtg cttctccagg
     3001 gaatgcagtt gcaaaagaat gggacaaaaa tggtaatggc tggattggat tttattacca
     3061 aaggggatat gatgcagctg gaagagttgt agctactaga tattcaacgt tataagttaa
     3121 ggagtgatgt ttttgatatc taaatcatta aaatcattaa aaacatttac taaaaagaat
     3181 ccgcaaatag ctactattcg tatttttata tttgctatag ctgttgctat aattgttaat
     3241 atgctaagcg gagggcaatt atacaaatct ggtttatttt tagtgttaat cttagttgtc
     3301 ttagacataa taaagtctaa aaaaaaataa atcgatacat tttagaagaa tagggttgtt
     3361 tgaatattac aaagcaacaa tttcaccttc ggtgaaataa gcgaaacttt acaaaaagtg
     3421 gctagcaaat gctagccttt ttttgtattg tggagcgtgg attttgaggg ggattcaagg
     3481 gggagcttgc gctcctttga caagcggtta tttgcaccaa atacggaggt atttggctag
     3541 caaatataga gcttgccaaa cccttttagt gagctttact cattgtacct ttttaggtac
     3601 aatggtattg cgaacgatac gtccgtagga cgtactgaaa gggtgggact tatgagcgaa
     3661 caacatcaaa atttggctag cgatcattct aaaaaatata cctatcgatc cgagccaaaa
     3721 caaatcagtt ttcgagtgag cgaatccgaa tttgcaaagc tgaagcagtc agctgaagct
     3781 ttgcaaatga gtgtgccggc tttcgtgaaa gccaaggcac aaaacgcgcg tctggtgaca
     3841 ccgaaagtgg cgccagacat tgcccaggca atcgcgcgcg atttagccaa agctggaggg
     3901 aatatcaatc aaattgccaa gtggtgcaat acacaccaac acgacgttgc tcctgatgat
     3961 gctcaacgtt tatccgaaaa cctaaaaatc atgcaaaagg agctacaaaa gatatggcaa
     4021 cagttaaagt aagtcgaacc acttcatgta gccgagcaat caattacgca gaaccacgag
     4081 caaccgtcaa aacaggaata aactgtgaca ttgattatgc caaaagtgaa atgaaacaaa
     4141 tacgcacgct ttatggaaaa gacgatcgtg tacaagcaca cttattgatt cagtcctttc
     4201 gaccaggaga aattaccgct gaaaaagcca atcaactagg ggcagagtat gcgaaaaaaa
     4261 tagcccctaa ccaccaaatc gcgatttaca cacatacaga caaagaccat attcataatc
     4321 acattgtcat taactccgtt aatcttgaaa ctgggaaaaa atttcaagcc catgggcaag
     4381 catttttaaa caaatgttat gacctaaatg acgagatttg tcttgaacat gacttaacaa
     4441 tcacggaacg aggaaagaaa accgaaaaac gaaccatgtc tgaaattaaa ttaaaagaaa
     4501 aaaatgaacc ggtttggaaa gacgaaattc ggtttgcgat tgatcaaaca atgaaaaaca
     4561 aaaaaactcg aacgtatacc caattttgtg attcacttaa aacattcggc attcattgct
     4621 tgaatcgcgg aaaaaatttt acttacgaat tggtccacaa aaagaaaaaa gtacgatcca
     4681 acaaactagg aaaggattac gaaaaggaga cgattttaca tgagctggac agacgagaac
     4741 gaacctacaa tcaacaacga accaacgagc tacgaagagc tcgagctagc attcgcgaaa
     4801 ctgcagaaga agtacgaaga gaacaacgaa cttttacgcc tgaacaatcg gaaattagac
     4861 cgactcgaag aaaccatgaa caacacgttg aacgaggaac agaccaccaa caagaattat
     4921 cgctctaaaa cgttaaaaga catcgaaaac gaaataaaga gacaacgtgc ctttcttgcg
     4981 ccttataccc aagaaaggat acaaactacg atggattcac aagtcaaaaa actccaccaa
     5041 gcgctattag accagcgaaa ccaagaacaa aaaaaggctt taattcaacg atcgatggat
     5101 attcttgccc ccttatgttg cttagtacta acattattag ccttttggtt ggtatgggga
     5161 gaataaacag acatggcatt ctatttaccc tatctactca tttctgccag tattttagga
     5221 attatttggc ttagctataa ggcttatcaa acaagatatt cattaaaagg ctctaaaatt
     5281 cgatttaagc gatttttatt ggtcggggtt atatttgcct tatcaatcgt tttaagtggt
     5341 ttattcggcg ttttagaggg taataaacgt gtttcaagaa gcattttatt aggggatatc
     5401 actcaaaagt atgaagcagc atgtgataaa aagaaaaaag agcaagcatt agcacaaaaa
     5461 atggaggaat ttaccgcttg ttatgaggac atgaacaata tttttgtgga tcaagagaaa
     5521 cgtttaacag ataaaaacat gaaaaaactc actcgttttt atcaaaactt accagaaaaa
     5581 cagcaaaaag aggtacaaga aaaatatgag caagtaaaaa aagacgtgca atattttaaa
     5641 gatacgcaga cagaagaagc ttgttgtaac ttatttagcg atacaatccc tttttcaacc
     5701 agtgaacaag aacgaaaaga acggcaacaa tcggtcacat acgaacgtta tgaaacactg
     5761 cttcagcaag caacaaacat acaaaatcca acgaaaaaag aaacggcatt aaattatcta
     5821 gaaagtgtca aggaatggtt ggatcagcaa caacaaaatt gaatttgatt agcaatcatg
     5881 ttaaactgaa cctgcaaatg atcaaacatt agatacacga aagccccaga gaggtcggat
     5941 tctctggggc tttttttcag gttgatgtcg cctttattga ttttacttct tgtttcggtt
     6001 attcaaccaa taactgaata aagagacaca aacttctaca agaagggggc aaatgaaccg
     6061 ttcaaacatt agatacacct ccttccagtc gcaagactgt cggataggcg acaagttatt
     6121 ataccttaca aaataaaatc tgtgtggtgt ttttaagtat cccttatttt cgggttgtta
     6181 gggcttgccc tgaccgcctg taaggcgctt taagaacaag ataaggtttt ttacccaaga
     6241 ctgtcttaaa acgacttaga cgagctatca gaggcttccc ccacctccgt tactgacttg
     6301 ttt
//
