LOCUS       NZ_CP084185             4461 bp    DNA     circular CON 22-AUG-2023
DEFINITION  Enterococcus faecium strain 4995/20 plasmid p4995_5, complete
            sequence.
ACCESSION   NZ_CP084185
VERSION     NZ_CP084185.1
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 4461)
  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  JOURNAL   Unpublished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 4461)
  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 4461)
  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
            CP084185.1.
            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..4461
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="4995/20"
                     /isolation_source="hematoma"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p4995_5"
                     /geo_loc_name="Poland: Bydgoszcz"
                     /lat_lon="53.1234 N 18.0084 E"
                     /collection_date="2020-09-25"
                     /collected_by="National Medicines Institute"
     gene            join(4264..4461,1..726)
                     /locus_tag="LDJ74_RS15685"
                     /old_locus_tag="LDJ74_15685"
     CDS             join(4264..4461,1..726)
                     /locus_tag="LDJ74_RS15685"
                     /old_locus_tag="LDJ74_15685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /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_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            742..1281
                     /locus_tag="LDJ74_RS15690"
                     /old_locus_tag="LDJ74_15690"
     CDS             742..1281
                     /locus_tag="LDJ74_RS15690"
                     /old_locus_tag="LDJ74_15690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /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_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            1962..2135
                     /locus_tag="LDJ74_RS15695"
                     /old_locus_tag="LDJ74_15695"
     CDS             1962..2135
                     /locus_tag="LDJ74_RS15695"
                     /old_locus_tag="LDJ74_15695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318189.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            2540..2974
                     /gene="bacA"
                     /locus_tag="LDJ74_RS15700"
                     /old_locus_tag="LDJ74_15700"
     CDS             2540..2974
                     /gene="bacA"
                     /locus_tag="LDJ74_RS15700"
                     /old_locus_tag="LDJ74_15700"
                     /inference="COORDINATES: protein motif:HMM:NF041453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     Typing          2..726
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttagtagca cgtatgacaa attattaagt attaatgctt ggaatgatga tggaaatact
       61 ttaactaaat ttgttgcttt cacaaaatat agcattatac gagataaaca acttgttata
      121 atttcagtta atccagaatt taaaggactt tttaatcaat taaagaactg gacaagattt
      181 aatctagagc aatttactaa tttggatagc acatattcaa aaactatgtt tcgattatta
      241 aaacaatatc gaactcaagg ctggactgaa ttttccaaag aaaaattttt tgatttacta
      301 gatattccta aaagttattg gaatagtccg tcaaatattg acaaatttat cttaaggcca
      361 attaaagaag aactcactcc cttatttaaa ggattaacta ttcgtaaaaa atatggtaaa
      421 ggtcgaggta aacctgttat cggttatcgt tttacttgga aagctgaaat taaccatgct
      481 gacgattttt ccaaagggaa acaagaagat ttacgtataa aattatttaa tattgatcac
      541 aatggagaat taacacgaga agaaaaatgg cgcgctaaag atcgaatact aaatcttccc
      601 ttaggcactc atgaagctga ttttaaacaa caacaacaaa ctgaagaaaa acaggcagaa
      661 aaacgagaac tttcaaacaa actcaaacaa gatttactag gaaatttaca aaacttattc
      721 gattaagctt aaggagtatt tatggcagat aaaacaatca aagaacttgc ggaagaatta
      781 ggagttagta aaacagcaat taacaaaaaa gtttctgaca aaaatcgaaa actttggttt
      841 gcaaaaaacg gaaacaagtt tgtgattaac gaaaccggtc aaaaagctat aaaatcaatg
      901 tttttagtcg ataacgcaaa cttaaatcga aaactagttg gcgaaaaatc aaaaaccaaa
      961 aaccataaaa acaccaacca agtttccgaa ttaaaactcc tttctttcct agaaaaacag
     1021 ttaaatcgaa aagatataca gctacaagaa aaagataatc aaataaaaca aatgcaaaaa
     1081 ttactcgacc agcaacaaca actcactcta caagcgaacc aacaaattga gaacctacaa
     1141 gaacagctcc atttaactta tacagaagaa actccaacaa ccgaatcaac tgccttttct
     1201 gaaaaaaaag cagacaatac acaaccactt attgaaaaaa agtggtggca aatttggaaa
     1261 tctaatagaa ccaatctcta aaattttcta gaagttagtt cggatagtag aggaaaaagt
     1321 tgtactacct gatggggaga tcactcaaat ttttatgaga aagaaaaaat agtttacaac
     1381 tgtaaacaat caatgtttat agttgtaaac tatcaaacta tatggtgact tattgcttaa
     1441 aataggttga aatctcactc aatttttggt ggaaaaacaa aataaattct aatcgatttt
     1501 gttgaaaaag tcataaaaaa acaaatgtga ttttaacaaa atttcaaaaa aatcgtttga
     1561 aatttcgttt attttttttg agaattttga tcatcgtagg gtcattgtag aatcattatg
     1621 agatcatcgt gggatcatcg aataaagtat gggaaaggct tgcggtgctt ggtattaagg
     1681 gcattctccg cctcccaggt tcttgaccat tttctcttat aagtgggatt tttaccacgt
     1741 tgagagaaaa tggtcaagaa cctgggaggc ggagaaaaca taccaagcac cacaagcaaa
     1801 aaaagttaga gtaacttcca aaaaagaaaa attttttaga acaacttttg aaaatttaat
     1861 tttgatttat atccgttcaa tttaaacatt tgataaactg aaggctagta tttaaaatgt
     1921 gtatacaagt ggtagcgtta aaaaaagtgg aggtataacc tatgttaaaa aaaactgtgt
     1981 tggtactggg ttctatttct ctaggaatat taggttttag ccccatgcta ttatccgtaa
     2041 ttggaaaaaa caattccaac agagaactta aattgaattc aaattattac aacagtccta
     2101 acgaagaatt gtttgtaaaa gaaacggata aataataaaa aagactgctc ttccgagcag
     2161 ccagttaaaa aataatgagt gtttattctt gaaaaagcaa cgcgcttata aagcgctacc
     2221 aaaaatttat catattttat gaaaaataac aatccagtaa aaaatgactg gtaaaaattc
     2281 acaaagaaac ggaaagaagc aactgcagaa aatcaagcct taaaaagagc tttttaccta
     2341 gaccaattaa aaatcacaaa gtgagcgtct ctatccattg gtagaggggc tacttggcat
     2401 agtgtacatt atgtctacta acctttaaaa taacacgttt tataaaataa accctcttga
     2461 caatatttaa ttttctgatt attctaaata tatacagaaa gcgctttcct aggattttat
     2521 atctaaggag gaagtaacaa tgaaaaataa aattattaaa attattactt gtctattttt
     2581 gttcggtatg attgttggag caagtactcc gttaaatctg tttcctttta gtgctagagg
     2641 tataaaagtg gaagctgcaa gttcacgata taatcataat catcgtggat ttacttgcta
     2701 taaaatgaac tattatgtta ctaataaaat gtgtagagat ttgaaaaaaa attataataa
     2761 gctaaagact cctgctcaaa ttgcatcttt tattcctatt ggtggagttg gaacatgggt
     2821 tattacaaat gcttttagta gtgctgttga tgcaatgaat gtctttgtaa gagctgcaaa
     2881 tcaaggaaaa ggtgtacaat taacatataa tgctcacttt agcaatacaa catcatatca
     2941 atacaatgat tacgctcgtt atgtaataaa ataatcagaa agtgaaacta tctcatgaat
     3001 aaaaagattt tagctgtaat tatttcaata atagttttaa tcactatgtt cttcatattt
     3061 aggctaattt tcaatataag cttacaaaaa agtattcttt atctaattcc tatagcattt
     3121 atcttagcaa tttttagaag tatttacgga aataaaaact ctaaatagct aaaaataaat
     3181 catactaaat tttacaaaaa gtggctagca ttttctagcc actttttgta ttgtggagcg
     3241 tgggttttga gggggattca agggggagct tgcgcccctt tgacaagcgg ttatttgcac
     3301 caaatacgga ggtatttggc tagcaaatat agagcttgcc aaaccctttt agtgagtttt
     3361 gtagaaagta cctttaaagg tactttcaca ttacgaacga tacgtccgta ggacgtactg
     3421 aaagggtggg acttatgagc aaattaatgc aaaatttggc tagcaaaaaa gctaaaaaat
     3481 atatgctaat aatcgagcga aataaacact ttttcaagtg agcgaatccg ccatgacaaa
     3541 gctgaagcag tttatttcag ctttgtcatg gcgtgtgccg acttttttaa aagtctaggc
     3601 acacgagcaa atatctttat caagctctaa tttgcgtttt aagacgtttg aaacgcctaa
     3661 gtatataaat atataagaat aggtttaaga gtgcttaaat cgaattttag agggcattta
     3721 gacaatttta gggttgttag ggcttgccct gaccgcctgt aaggcgtttt aagaacaaga
     3781 taagggattt atactaggac tgtcttaaaa tgtcttaaac gaacgctcag agcttctcaa
     3841 agggttcctt atgaacggct tttagcaaag gagccggagg cgactgcgca gtataatgtg
     3901 agagcagagc gatcacacct ttttagcgaa ccgtagggag caaggtttgg aattggcagt
     3961 tttgataaat tcgcgaacct gtttagagaa aaaaggagtg attttttagg cgggaaaatt
     4021 agcctcccct ctttttatat ctctttttat atctcttttt atatctcttt tatgtcggct
     4081 gtgtccttac tctcccaagc aattcagagt tttttcaagt aggttttcta cgcttttcaa
     4141 gtaggttttc tacgcttttc aagtaggttt tctacgcttt tcaagtaggt tttccgacat
     4201 tattgagtat ttttataaag tatgttactt ttatttcata ctttataaaa gtaggagaag
     4261 cttatggcaa atgaaattgt aaaatatgaa aatagattaa atcatattcc tctgagaaaa
     4321 tttaatagtc gtgaaatgaa cttatttttt tcaattgctt cacgtgtacg tgaaaaaggt
     4381 gtagatgaga ttattttttc atttcacgat ttgaaaaaac taagcggtta tacagaacgt
     4441 ggggaacaat ttataaaaga t
//
