LOCUS       NZ_CP093944             5946 bp    DNA     circular CON 11-APR-2024
DEFINITION  Enterococcus faecium strain NY2032 plasmid pNY2032-3, complete
            sequence.
ACCESSION   NZ_CP093944
VERSION     NZ_CP093944.1
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 5946)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY2032
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5946)
  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
            CP093944.1.
            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..5946
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY2032"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY2032-3"
                     /geo_loc_name="China: BeiJing"
                     /lat_lon="39 N 116 E"
                     /collection_date="2018"
                     /collected_by="a public hospital"
     gene            join(5790..5946,1..812)
                     /locus_tag="MPL11_RS15435"
                     /old_locus_tag="MPL11_15435"
     CDS             join(5790..5946,1..812)
                     /locus_tag="MPL11_RS15435"
                     /old_locus_tag="MPL11_15435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            829..1353
                     /locus_tag="MPL11_RS15440"
                     /old_locus_tag="MPL11_15440"
     CDS             829..1353
                     /locus_tag="MPL11_RS15440"
                     /old_locus_tag="MPL11_15440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /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_044383356.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTENHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KAEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            1729..2010
                     /locus_tag="MPL11_RS15445"
                     /old_locus_tag="MPL11_15445"
     CDS             1729..2010
                     /locus_tag="MPL11_RS15445"
                     /old_locus_tag="MPL11_15445"
                     /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_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2012..2428
                     /locus_tag="MPL11_RS15450"
                     /old_locus_tag="MPL11_15450"
     CDS             2012..2428
                     /locus_tag="MPL11_RS15450"
                     /old_locus_tag="MPL11_15450"
                     /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_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            3050..4204
                     /locus_tag="MPL11_RS15455"
                     /old_locus_tag="MPL11_15455"
     CDS             3050..4204
                     /locus_tag="MPL11_RS15455"
                     /old_locus_tag="MPL11_15455"
                     /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            4177..4620
                     /locus_tag="MPL11_RS15460"
                     /old_locus_tag="MPL11_15460"
     CDS             4177..4620
                     /locus_tag="MPL11_RS15460"
                     /old_locus_tag="MPL11_15460"
                     /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"
     Typing          2..808
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.698"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taagcaatta taaagcaact gcaaatgttc gattcataga tgatttagaa acaacgtatg
       61 acaaattaat ggatttacgt tttggtagaa gaagtgctga cggtttgcaa cgtgaacgtt
      121 ttgttttatt taatcaattt aaaatcgacg gaaaatctga tattcctttt gctgaaatac
      181 aagttcatga aaaagcctta cccttactta ataatcttga agaatgggtg cgctattctc
      241 tccaacaatt caatgaatta gaaagcagtt attcaaaaac aatgtttcga ttactaaaac
      301 aatacagaac caaaggtttc gcttattttt caaaagaaga ctttcatgaa ttacttgata
      361 ttcctaaaag ttacaaccaa ggtacgattg atcaacgtgt gttcaatcca atacgacaag
      421 aactaaccgc aatctttaaa ggtttaacaa tcaaaaagaa atacggaaaa ggacggggaa
      481 agcctgtcat tggctatcaa tttacattta aacctgagat aaaaaaatca gacgacttta
      541 acaaacatgc cccaacaaaa gaagaacaaa acaaagcatt agaactagct aaccaacaag
      601 ttcaatctga aaaagcacct acttcattac aagaaaaaat caaagaacaa aagcgaaaat
      661 tggaactttt acaacagtta gaaaagttag aaagagaaca aaatacccaa aataaagaaa
      721 ataatgcaca aaaatcagag ataaattccg atattccttc agaactaaaa aaagacttat
      781 tagacaatct tcaaaactta ttcaaagatt gaggggtttt tagattttat gacagaaaaa
      841 acaatcaaag aacttgctga agaattagga gttagtaaaa cagcaattaa caaaaaagtt
      901 tctgacgaaa atcgaaaact ttggttttcg aaaatcggaa acaagtttgt gattaatgaa
      961 accggacaaa aggctataaa atcaatgttt tttaacgaaa acgaaaactc aaatcaacaa
     1021 ctagttggcg aaaaaacgaa aaccgaaaac cacaaaaacg ccaaccaagt tcccgaatta
     1081 gaagtccttt ctctcctaga acaacagtta aatcaaaaag atatgcaact acaagaaaaa
     1141 gacgagcaaa taaaacaaat gcaaaaatta ctcgaccacc aacaacaact caccctgcaa
     1201 gccaaccaac aaatcgagaa actgcaggaa caactacagt tgacttatac ggaagaatct
     1261 tcggaaaata aatcaacgac tctttctgaa gaaacagaat cgatagaaaa acaatcaaag
     1321 gcggagaaaa aatggtggca attctggcaa taaaaccagc aatttaaatt aataaaaatt
     1381 gctggtttta ttcttctttt tgcttttgcg agcagagcaa catggaccca tgttgcgata
     1441 ttttggtggc gccccaatcc ccgttttttc gttgaatctt actcggactg cactcgtttt
     1501 acagctgatt tttctgaatt ttgaaagagc ataaggaaac gtggtatcac tttcttacga
     1561 aaggtgctag ataggctgtg cctatcacgt ttctcagaaa aaaatttgct atcacttttt
     1621 tgccattgtg gctaggctat gtatagtgtt ttggcgaaaa atagctatac aaatactata
     1681 tttgtatggt atacataaat tatacgctga tacgaaagga aaatttccat ggacatttta
     1741 gttcgaaata tcaatcccaa aattattgca agaatagata aacgttgtca ggaactcaca
     1801 accaaaacgg gcaaaaaatg gagtcgaaat aaatatctaa aagttctaat cgaaagtgat
     1861 tttgaccgtc aacttatgaa ttacaaaaaa gatcaattcg atttattact cgaaaaattt
     1921 attgccattc aaacagaaaa tacgaacata ctgaatgact atgttcacac aaacaaccaa
     1981 ctcattgaaa cacttatcgg aggaatataa catgagaaaa acttctgttc aaaaacacgt
     2041 aaccctttat cccagtcacg ttgacgtttt agattccatc atcgaaaaaa atccagacgt
     2101 caacaattat tcagaagcca ttcgtttttt atgtatgagt tatgaacctg ataccaatac
     2161 aaccacaacc agtaaccaag caaaactcaa tgccatggga aaagaaattt ctatcatgac
     2221 agaaatcatg gcagaatttg ctgatttata tctaaaagat actggtgttc ttatcggtac
     2281 aaattctaaa gtgtatcaag aagtgaaaga aaaaattgaa aatcaactca atccttcccg
     2341 acgaaatcaa cccaaaaatc gtcaaaaaga aaccaatcaa acctttactt ctggaaattt
     2401 tgacccaaca aactttctaa aaagataaaa aaagaaaccg atccctaaaa aaattcctcg
     2461 atttcttttt agggatcagt cttccagcaa gatttgcaag ttggtaccaa cttgcgaaaa
     2521 aaaagaaaaa tccgcttatg caacttcttc tttttgtatt ttgaggcgct accccaatcc
     2581 ccaagtatcg gttatttaat agcgcggaaa tccaaagaat aggacgtacc ctgaaacaaa
     2641 aaaagactgc tctcacgagc agcccaaaat gagattatcc tattcatcaa cataaaaata
     2701 ttacaaagtg aagaactaga gaaagacaaa aaaagcatat caaatcctct caaaaataac
     2761 aagtctttaa aaaatgacag ataaaaatgc acaaagaact aaaaaagaga aatcgcgtaa
     2821 aatcaagcat tagaagctag taactagcta gaccaattaa aaatcacaaa gtgagcgtct
     2881 ctatccattg gtagaggggc tacttggcat agtgtacatt atgttaacta acgctataaa
     2941 taacgattat gttcccaaaa caatatttta tgaactataa caaaaatttg ttatcgcata
     3001 ttgtatattt taattatagg tgtataccac ttaaatttaa cacaaaggcg tgattatttt
     3061 gaaacccaaa aagaaaattt atctaggtct cctcttttcc ttgatgattg gaatttttag
     3121 tataggaatt acaaatacct atgcttcaga aaattctaat ttcaatatca actcccaacc
     3181 aattgaagaa caagcaatta attttgcgaa aactgatttt gaacactcca taacttcaat
     3241 tcttttaatg gaaaataaca ccgaaactga tattaactat actcttggtt cgccatttaa
     3301 aatgctcgat ggagaaaata cggcaaatag ttctattttc tttccagtat tttcagacgc
     3361 tgataatacg attaaatata tttataccgt caaaaaaaat acaaatggag aatattcagg
     3421 aagtatttca caatttttag caaaagaact tcaaaatcta gtagatagta atataacaga
     3481 tacaacctta ttttttcaag ataatagcat ttattattcc gataatggac aaattaaact
     3541 actttggaaa tcacctttaa gtacagaaaa aaatggtgtt tcttccttta cagaaaaaaa
     3601 tgatcttata tccgtaaata taaaaaataa aattaaaaat ttctctaaaa aacaaaattt
     3661 tcctgcggtt aaacgtgtaa aaagtgtctc ctccggagat aactttatta tgattaattg
     3721 gcgtatagca gaaacccaaa caagttttcc gtggtgtgct gcttacgtag aagctgctat
     3781 cttatgtaac aaaacagatg tacatgctac ttcagctaga gccattatgc attataccta
     3841 tcctaattta aacaacagtc aaattgaatc aaaaagtctt aatcaagatc aaataataaa
     3901 atatgcaaat tactgtggtg tttatcctaa aaaagtagca cgaatactaa acctttcaga
     3961 ggtccaaaca caactaagaa aaggaaatgc catttatatg ggaactgctg gttatggaaa
     4021 ttatagtaac agccgtcatg cacttgcatt atttgggtgg gtcaatcaag gtggttatca
     4081 aacttactat gtgtggaatc cttggtataa ctacccaact gtaataagtg caaatgcagg
     4141 accagttaca attcctgtac ctggaggtgg ttttacttgg gacaatacca ttacaaattg
     4201 gtaaataaac ccattgcttt agttatgggt ctagtgttag ttcttttctt aactagttgt
     4261 tcaaaaaaac aagaaataca aaagactgat ctgattcctt ttctaggaac ttggcaaact
     4321 aaagatcatt cagaacgtct agtaatcact aatttaaata cttcaaaaaa tatagaacaa
     4381 tataccatct tagtaaaaga gaacaatcat aaaattcaaa tcattgataa aaatttaaat
     4441 ataaatgaac aagttttcat ttacaaagca acaaataatt tactaacact gcgctctaat
     4501 aaaaaacaat tagattacac ttttagtttg gattctccaa aaaagctcgt atttattttg
     4561 acaacgaatg atgggacaga agggacagct aaaccaattg aattttttaa agctgattga
     4621 tgaatagttg tttgatatta caaaacaata atttcaccga aggtgaaaca agcgaaactt
     4681 tacaaaaagt ggctagcatt tgctagcctt ttttgtattg tggagcgtgg gttttgaggg
     4741 ggattcaagg gggagcttgc gcccctttga aaagcggtta tttgcaccaa atacgtaggt
     4801 atttggctag caaatataga gcttgccaaa cactttagtg agttttgtag aaagtacctt
     4861 taaaggtact ttcacattac gaacgatacg tccgtaggac gtactgaaag ggtgggattt
     4921 atgagcgaac taatgcaaaa tttggctagc aaaaaaagtt aaaaaatata tgctaataat
     4981 cgagcgaaat gaacactttt tcaagtgagc gaatccgcca tgacaaagct gaagcagttt
     5041 atttcagctt tgtcatggcg tgtgcctaga cttttaaaaa agtcggcaca cgagcaaata
     5101 tctttatcaa gctctaattt gcgttttaag acgtttgaaa cgtctaagta tataaatata
     5161 taagagtagg tttaagagtg cttaaatcga attttagagg gcattcagac aactttaggg
     5221 ttgttagggc ttgccctgac cgcctgtaag gcgctttaag aacaagataa gggatttata
     5281 ctaagactgt cttaaaacgt ctcaaacgaa ggctcatagc ttctcaaaga gttccttatg
     5341 aacattttta gcaaaggagc cggaagcgac tgcgcagtat aatgtgagag cagagcgatc
     5401 acaccttttt aagcgactgt agggagtaag attcccagtt gagaaaaatg cgcgaatctg
     5461 tttggagaaa aaagaagtgg ttttttaggc gggaaatttt gtccccctct tttataatct
     5521 ctttttaaac ctctttttaa acctctttac cgtcggctat atccttactc tcccaaggga
     5581 atgacgcttt tatctacatc gttttgtctg tttatctaca tcgttttgtc tgtttatcta
     5641 catcgttttg tctgtttatc tacatcgttt tgtctgtttg tacattgaat tagtacatcg
     5701 acgatgttaa tataagatgt agataaacag gcattttgta tttcataacg tgtatctctt
     5761 gtgcgagtaa gaaaggagct attttaaata tgtctaatga aatcgtaaag tatcatcatg
     5821 aattaaatac aattccgttg cgaaaattta caccagtcga aatgaatttg ttcttttcta
     5881 tcgtatcaag aatgcgtgat gtaggtgata aaaaagtaca atttacattc gagcaattaa
     5941 aagatt
//
