LOCUS       NZ_CP084186             2056 bp    DNA     circular CON 22-AUG-2023
DEFINITION  Enterococcus faecium strain 4995/20 plasmid p4995_6, complete
            sequence.
ACCESSION   NZ_CP084186
VERSION     NZ_CP084186.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21850488
            Assembly: GCF_020221735.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2056)
  AUTHORS   Wardal,E., Sadowy,E., Zabicka,D. and Hryniewicz,W.
  TITLE     Vancomycin-, tigecycline- and linezolid-resistant Enteroccoccus
            faecium carrying both vanA and vanB genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2056)
  AUTHORS   Wardal,E., Sadowy,E., Zabicka,D. and Hryniewicz,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-OCT-2022) Molecular Microbiology, National Medicines
            Institute, Chelmska 30/34, Warsaw 00-725, Poland
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 2056)
  AUTHORS   Wardal,E., Sadowy,E., Zabicka,D. and Hryniewicz,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-SEP-2021) Molecular Microbiology, National Medicines
            Institute, Chelmska 30/34, Warsaw 00-725, Poland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-FEB-2021
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 670.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/21/2023 08:47:26
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,050
            CDSs (total)                      :: 2,960
            Genes (coding)                    :: 2,831
            CDSs (with protein)               :: 2,831
            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)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 38 of 129
            Pseudo Genes (incomplete)         :: 86 of 129
            Pseudo Genes (internal stop)      :: 34 of 129
            Pseudo Genes (multiple problems)  :: 25 of 129
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084186.1.
            Bacteria and source DNA available from Molecular Microbiology,
            National Medicines Institute, Chelmska 30/34, Warsaw 00-725,
            Poland.
            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..2056
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="4995/20"
                     /isolation_source="hematoma"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p4995_6"
                     /geo_loc_name="Poland: Bydgoszcz"
                     /lat_lon="53.1234 N 18.0084 E"
                     /collection_date="2020-09-25"
                     /collected_by="National Medicines Institute"
     gene            complement(join(1984..2056,1..149))
                     /locus_tag="LDJ74_RS15705"
                     /old_locus_tag="LDJ74_15705"
     CDS             complement(join(1984..2056,1..149))
                     /locus_tag="LDJ74_RS15705"
                     /old_locus_tag="LDJ74_15705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299940.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002299940.1"
                     /translation="MRVIKSEKFTLAEIMTTSELAQELDYNQAYVLRLAKEHLTEGKEY
                     RSAGRRNYLFSPEALKKLEKVITTKEGE"
                     /name="hypothetical protein"
     gene            766..921
                     /locus_tag="LDJ74_RS15710"
                     /old_locus_tag="LDJ74_15710"
     CDS             766..921
                     /locus_tag="LDJ74_RS15710"
                     /old_locus_tag="LDJ74_15710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299939.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CopG family transcriptional regulator"
                     /protein_id="WP_002299939.1"
                     /translation="MISNEKKRVVVTLTKEVADNLDKIAKQMGLSKSGLITIWVNANGK
                     ENEQKK"
                     /name="CopG family transcriptional regulator"
     gene            988..1590
                     /locus_tag="LDJ74_RS15715"
                     /old_locus_tag="LDJ74_15715"
     CDS             988..1590
                     /locus_tag="LDJ74_RS15715"
                     /old_locus_tag="LDJ74_15715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_002323513.1"
                     /translation="MTSRKTKDERTRNWTFVVYPESAPENWREFLDELHVPWVESPLHD
                     KDVNPDGELKKPHWHVLIMFSGKKTYDQIREITQKLRSPNPQKCANAKGMVRYFAHMDN
                     PEKFQYAKSDIIAHGGAEIASYLSVTSAERYELIREMMSFVDSKNITEIKDLIDYAMSE
                     RFDDWFPLLCDNSAYIIGQYIKSNRHGGSVNSKINKG"
                     /name="replication protein"
     gene            complement(1726..1983)
                     /locus_tag="LDJ74_RS15720"
                     /old_locus_tag="LDJ74_15720"
     CDS             complement(1726..1983)
                     /locus_tag="LDJ74_RS15720"
                     /old_locus_tag="LDJ74_15720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002377879.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002299941.1"
                     /translation="MPKETTINVEQLEKLLESYSNDFIELTGGKVEETTDLFDLLLTNI
                     LELNSEEQKEHKGKLIAPSYRKVAKSAVPTGFLTKQPYIF"
                     /name="hypothetical protein"
     Typing          complement(1649..1824)
                     /name="MOBV"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.01e-87"
     Typing          989..1518
                     /name="rep_cluster_2351"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ctaccggcag agcgatattc ttttccttca gtcagatgtt ctttcgctaa gcgcaaaacg
       61 taagcttggt tgtaatcaag ttcttgtgca agttcgctgg tcgtcataat ttcggccaaa
      121 gtgaattttt ctgattttat cactctcatt tatgctcctt ccatttaacg tccgtctata
      181 ttacgtgagt acgtcggact tacgacataa gcttataata taagttttct gtgttgtggt
      241 caattttata ttatcgaaat gactagtaga aaaaatcaat gctctaaaaa gggtctattt
      301 tgcgttttaa gcgatttagc gtctatttcg tttagttatc ggcgcaatcg ttaaaacacg
      361 taagagaagc gagaatggag cctgtaaggc gactggtagc gaaacggtcg tgttagattg
      421 caaaagccga tagctgaacg aaatagtaag cgtggcgcct gcatatattt cggtagaagg
      481 aggtcggggt tcggggcgga gccctgaggt ttgttttttg gttttggtgt ttatgaattg
      541 ggcggaggag ggggggacta cgacaccccc cttattggtc attggtcatt ggtcgatagc
      601 tgtttagcct tactctccca agggtttcag cgtttttttt tgacaaaatc agtaatgtca
      661 agggtttaag gcctattatt cgctaattag tatctaaact gttgcacctt agttactttt
      721 ttgttactat ggtttttaag aaaaagtcgt tggaggatac gaattatgat cagtaatgaa
      781 aaaaagagag tcgttgtaac gcttactaag gaagtggcag ataatcttga taaaattgcg
      841 aaacaaatgg gtcttagtaa gtctggtctt attacaattt gggttaatgc taacggaaag
      901 gaaaatgagc aaaaaaaata gcaaaagcat tagtgttggc gcactgcttt tgctgttaga
      961 ctgttgttca attaaggtaa ttatagcatg acgagtagaa aaactaaaga tgaacgcaca
     1021 aggaattgga cgtttgtagt ctatcctgaa tcggctcctg aaaattggag ggagttttta
     1081 gatgagttac atgttccttg ggttgagagt ccacttcatg ataaagatgt gaatcctgac
     1141 ggtgaattga aaaagcctca ttggcatgtt ttgataatgt ttagcggtaa aaagacgtat
     1201 gatcaaatac gtgagataac tcaaaagctt cggtctccaa acccgcaaaa atgtgctaat
     1261 gcaaaaggta tggtgcgata ttttgctcat atggataatc cagaaaaatt tcaatatgct
     1321 aaaagtgata ttatcgctca tggtggtgca gaaattgcta gttatttgtc agtaacgagt
     1381 gcagaacgat atgagttgat tagagagatg atgtcgtttg ttgattctaa gaatatcact
     1441 gaaatcaaag atttaattga ctatgcaatg tcagaaagat ttgatgattg gtttccgctt
     1501 ctttgtgata attcagctta tattatcggg caatatataa aatcgaatcg tcatggtgga
     1561 agtgtaaatt caaaaataaa taaaggataa gagctgttaa tttcagctct ttttttgtgc
     1621 gtgaaagtct tagtcactat gaccaaaact acggacgaaa ctatgaccaa aagtaggtac
     1681 tatattatga ccgaaaatag gtccaaaatg gatttttttg tgatatcaaa aaatataagg
     1741 ttgttttgta agaaaaccag ttggcacagc cgacttagcc accttcctgt aggaaggtgc
     1801 tatcagtttt cccttatgct ctttttgttc ttcagagttt aattccagaa tatttgtgag
     1861 aagtaggtca aagaggtcgg tggtttcttc gacttttccg ccggtcaatt cgataaaatc
     1921 attggaatat gattctagca atttttctag ttgttcaacg ttgatagttg tttctttagg
     1981 catttactca ccttctttgg tggttatgac tttttctagt tttttaaggg cttctgggct
     2041 gaaaagatag tttctt
//
