LOCUS       NZ_CP094234             4375 bp    DNA     circular CON 11-APR-2024
DEFINITION  Enterococcus faecium strain NY13320 plasmid pNY13320-4, complete
            sequence.
ACCESSION   NZ_CP094234
VERSION     NZ_CP094234.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26755017
            Assembly: GCF_022749455.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4375)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY13320
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4375)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-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_022749455.1-RS_2024_04_11
            Annotation Date                   :: 04/11/2024 17:08:02
            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)                      :: 3,029
            Genes (coding)                    :: 2,884
            CDSs (with protein)               :: 2,884
            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)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 70 of 145
            Pseudo Genes (incomplete)         :: 66 of 145
            Pseudo Genes (internal stop)      :: 35 of 145
            Pseudo Genes (multiple problems)  :: 20 of 145
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP094234.1.
            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..4375
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY13320"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY13320-4"
     gene            111..1517
                     /locus_tag="MPN36_RS15220"
                     /old_locus_tag="MPN36_15220"
     CDS             111..1517
                     /locus_tag="MPN36_RS15220"
                     /old_locus_tag="MPN36_15220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002333830.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1966..2940
                     /locus_tag="MPN36_RS15225"
                     /old_locus_tag="MPN36_15225"
     CDS             1966..2940
                     /locus_tag="MPN36_RS15225"
                     /old_locus_tag="MPN36_15225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_044384214.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLKYQSLTLPLKMQWSIDRITIVGK
                     LKENIYYHTPNDVLILNFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKIVPPEITTWWRLELQLRRG
                     KATDWHEMVHESLDSFASPHYFPPNTKVTERIMVKGLLYDHSEWGNLAKNTKKKYRDLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2937..3170
                     /locus_tag="MPN36_RS15230"
                     /old_locus_tag="MPN36_15230"
     CDS             2937..3170
                     /locus_tag="MPN36_RS15230"
                     /old_locus_tag="MPN36_15230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303408.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            3163..3582
                     /locus_tag="MPN36_RS15235"
                     /old_locus_tag="MPN36_15235"
     CDS             3163..3582
                     /locus_tag="MPN36_RS15235"
                     /old_locus_tag="MPN36_15235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_044384217.1"
                     /translation="MTDLSEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVVRSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            3591..3899
                     /locus_tag="MPN36_RS15240"
                     /old_locus_tag="MPN36_15240"
     CDS             3591..3899
                     /locus_tag="MPN36_RS15240"
                     /old_locus_tag="MPN36_15240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            3903..4265
                     /locus_tag="MPN36_RS15245"
                     /old_locus_tag="MPN36_15245"
     CDS             3903..4265
                     /locus_tag="MPN36_RS15245"
                     /old_locus_tag="MPN36_15245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     Typing          1991..2921
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.854"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          112..1514
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttggaattg tgacagccat gtcacaatta ggaaaatgtt actctttgac aaagagtaac
       61 agaaaggttt acactctttt tattagcgac agccgaagga gggttttaac ttggggttca
      121 gtatttcgtt caaaaaggga acaaagaata caagcatttc tcataataat cgtgagttaa
      181 ctgatagcca aaaaatcaat gactggcata agcatattga tttcacaaaa tcggatgaaa
      241 atatctattt agaacaaaca aatattcgtg aaaaatatga agaattattc ggtgaagccg
      301 tagaaaaata taatgcaaag cagaaaagag ccgatagaaa aatcgaggac tatttagcaa
      361 aggttcgcaa ggataaaaaa ttggaaccac agcgagaatt tatcgtgcaa attggtactc
      421 ttgatgattt tcgtactact cgtgatgatg gttcttctac tggcatatcg gaacaacaag
      481 cagaacaaaa tcgagtgatt gccaacaaaa ttttagttga atatttcaaa gaatttaaag
      541 aacggaatcc taatttatcc gtctacaatg ctgttattca taatgacgaa gtaagtccgc
      601 acctgcattt gaatattgtt cctgttgctg aagggtataa acggggtgtt caaaagcaac
      661 caagttttaa caaagccttg caacagcagg gtttacgagc agataaagag aatggtcgag
      721 tgatttggaa taattttagg aatcaggaag ttgagtcaat tgaacgtttg atggcagatt
      781 ttggttggga gcgtgagtta gtcggtacta acaaaatcaa agatgttcac gaatataaag
      841 aaatcatgag cgagatttca gaattgcgtc aaacggccgt aaaagagcgt gagagcgttt
      901 ctgatgagtt gaggtatatt tctaggcaaa gagaagaaaa tgagcgagaa aaggctctgg
      961 tggcttctga gagagtgaag attgaagaag agaagaaaaa tatgctgaat gtaaaaaaag
     1021 agatggcggt cattttccaa aaagatattg ttcctttaga aagtttcaag aggcttcctg
     1081 atggttcgta tcatttatct gggaatgatt ttgttgattt gtatcaacga gctacgagag
     1141 caacaaatgc caagagaaat gctgataaca tgagtgagca atatttacag atgcttgagc
     1201 aaaatacaga attaaatgag tatgtagcta cattggaaga agagcgtcat ttgtctggta
     1261 gaaaacaatt agcagattta caagtggaaa ataaaaagct gaaagaagaa aatcgctctt
     1321 tacgccagcg tttagagcga ttaaaaaacg catttcaaaa atcgatcact cgtttgtcta
     1381 tccgttttgg tcttgcagaa aaggatatgg ggctttctga ggaattagaa gtgttagagc
     1441 aggagaaaac cttattttat cgtcaaaacg tctcacagcg taaattagag cgttctgaag
     1501 atgagatcga gtggtagtta cgatgtgcag tcaacggtac cggaggcggt ttgtgccgag
     1561 gataaggagt tgacggctaa accactaatc cctgaagctg acatttgcta aaaaatggca
     1621 agtccatttt ttggccaacc tagcgttagc gaagtttggg ggcgcccttt tcaaagggtg
     1681 cggttttatt ttttggatat ttgcatagct aaagagaagt gctattattg agttatcaaa
     1741 taaataaact gaaaaaagag caaaaaaata aagtcgagca acgctggaca cgttctcgac
     1801 ctttacggaa actaatcgca ctagctccgt aacttcttaa tcattatacg aatattttta
     1861 gatttcttca agactagaga ttttttggta atgaattttt aagagttacg tgaacttttg
     1921 aaaattcttt ccagaagtct ctttttcttt gaggaggaac aaaatttgag taaaaaaggc
     1981 acgatcataa atgagtggga aaaattaaca gccccctcta acaggcggtt aaagtatcaa
     2041 agtttgaccc ttcccttaaa aatgcagtgg tcaattgacc gaattaccat agtcggaaaa
     2101 ctgaaagaaa atatttatta tcacactcca aatgatgtgt tgattttaaa ttttgaacag
     2161 cttatgcgcc taaatgaagg taatggttat ttaagatctg ttagtaataa tggttggcag
     2221 ttgttagacc aacatgaaga gaatattgct tatattgaaa ttttaaaatg gcaagagggg
     2281 aaagggcgta tagacttcaa tccgaataag attagtcaat tcttagctag ttccatgaaa
     2341 aattttattc atgatttgtt tatcgaacct cacttttcac gtgcggatat tgcttgcgac
     2401 attatcgatg tacctgatga gtttattaca caatatcggg tagttgatcc tgtgtctttt
     2461 aaaccaattt atgggcgttc tggtaagtta gaaacggcat attggggtag tcgtgccagt
     2521 gaacgacaaa ttcggatgta taataaaaaa ctggaacaag aaagaaaacg taaaattgtt
     2581 ccgccggaaa taacgacatg gtggcgacta gaattgcagt tacgaagggg aaaagcaact
     2641 gattggcatg agatggttca tgaaagtttg gatagctttg ctagtccaca ttattttccg
     2701 ccaaatacta aagttactga acggattatg gtgaaaggtt tgctttatga tcattctgag
     2761 tggggaaatc tagctaagaa tacaaagaaa aaatacaggg atttgttgaa gcaagaaagt
     2821 caaaatgatg aattgacgaa tcatttgcga gaaacctttg cggaatcggc agacgattta
     2881 aaaaaagaat tagacacatg gcttctaggg ctagacgtaa cagaggagga agaaaaatga
     2941 cagaaaaaca aaagtatttt ggtaagaaaa attggttggt aaatttaaca ggtgattacg
     3001 ttgtggttgt ttttttggat agcaaaaaaa tgtccggtaa gttacttgat gtaacgcaat
     3061 atgaattgat tttgaaaaat aataaaattg actctccgat tattatccct aagcacgccg
     3121 ttaaatatat ttatgcggta gctgaaagta gtggagaagc taatgactga tttgtcagaa
     3181 aagatgacca taaaaaatct tgctgacgaa ttgggtgtat cgaaaaatac agtgcgcaat
     3241 caactggtca attcagggtt tgaccttgct cagtataaag aaaatggcat tatcatgcta
     3301 gataaagagt tgattggtgt tgttcggtca atttatcggt caaaaagtga tcaattgact
     3361 ggtcaattac cggtcaataa cacaggcagt gattttcctt tagaaaaaga gaatgagttt
     3421 ttgcgtgatc aattagctga gaaggacaaa catatttctg aattaacaga aatgattcgt
     3481 gatcaacaaa aattgaccct gcttcagcaa caaaaaaacg atcagttgtt actagaaaat
     3541 caagaattaa aaaatcgaaa atggtggcaa ttctggaagt gaggtgtgac atggataaaa
     3601 ttgatttgag agaagaaaca gtcgatagaa ttgaattgat gtatgaacgg ttagctgatt
     3661 atttgaattt gccggatgaa gataattata gtgaaatgct tgaacgaatt atggatgttc
     3721 tcaactcggt tatcaatgct gatttagcaa aatcttcagt tttgactaat gaatttgttc
     3781 ataagcattt agcgcaaaca actgatgaat cagaaaaaga attttggttg aaattaatga
     3841 gtcatgttat gcagttaaac caaatttccg ttattaattc caaagaaaag gagatgtagt
     3901 ttatgggaat gactttagca gatattaaag cgcaagaaga aaaattaaaa aaagaacaag
     3961 cgaaacttcg ccaacagaaa aaacgcttga ttgagaaaga aaatgctgca atgggcaagg
     4021 ctcttcggaa gcgttttggg tttgaaactt ttgctgattt tgagcggtgg ctatcgtcga
     4081 tttctgacga tcagcaacac gaaaaatcag tggataatga gtggcttgct gatgaaaaat
     4141 cagcgccaag cgaacgagat tatcccgatg aatctgacgg cttattcgga gtgataccga
     4201 ataagaaaag tcagatgagt gagagtaaat ttacgtcaat atttaatgac gtgaatttac
     4261 gataagcgat tattttgcgt gaagcaaaat aaagcgtaaa aggagttgag agcgtgacac
     4321 gctttcggct ccttttttcg ttgtcacttg tgacagcgaa taccctcgga gagca
//
