LOCUS       NZ_CP119158             4587 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain GENOMIC22-005 plasmid pCFSAN126950_08,
            complete sequence.
ACCESSION   NZ_CP119158
VERSION     NZ_CP119158.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33438667
            Assembly: GCF_029167665.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4587)
  AUTHORS   Hoffmann,M., Luo,Y., Sorensen,L.H., Pedersen,S.K. and
            Hendriksen,R.S.
  TITLE     Results of the 2020 Genomic Proficiency Test for the network of
            European Union Reference Laboratory for Antimicrobial Resistance
            assessing whole genome sequencing capacities
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4587)
  AUTHORS   Hoffmann,M., Luo,Y., Sorensen,L.H., Pedersen,S.K. and
            Hendriksen,R.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-FEB-2023) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Microbial Genome Analysis v. SMRT Link
            11.0.0.146107
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 700.0x
            Sequencing Technology             :: Pacbio Sequel IIe system
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029167665.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 06:43:33
            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)                     :: 3,199
            CDSs (total)                      :: 3,108
            Genes (coding)                    :: 2,968
            CDSs (with protein)               :: 2,968
            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)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 43 of 140
            Pseudo Genes (incomplete)         :: 88 of 140
            Pseudo Genes (internal stop)      :: 37 of 140
            Pseudo Genes (multiple problems)  :: 21 of 140
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119158.1.
            Bacteria and source DNA available from Sorensen, Lauge Holm,
            lahoso@food.dtu.dk.
            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..4587
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-005"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1352"
                     /plasmid="pCFSAN126950_08"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            52..1458
                     /locus_tag="P0D82_RS15895"
                     /old_locus_tag="P0D82_15890"
     CDS             52..1458
                     /locus_tag="P0D82_RS15895"
                     /old_locus_tag="P0D82_15890"
                     /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_002304901.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQINIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKMEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYICRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1907..>2026
                     /locus_tag="P0D82_RS15900"
                     /old_locus_tag="P0D82_15895"
                     /pseudo=""
     CDS             1907..>2026
                     /locus_tag="P0D82_RS15900"
                     /old_locus_tag="P0D82_15895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /name="replication protein"
     gene            2332..3321
                     /locus_tag="P0D82_RS15905"
                     /old_locus_tag="P0D82_15900"
     CDS             2332..3321
                     /locus_tag="P0D82_RS15905"
                     /old_locus_tag="P0D82_15900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_116632605.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELIESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     gene            3318..3737
                     /locus_tag="P0D82_RS15910"
                     /old_locus_tag="P0D82_15905"
     CDS             3318..3737
                     /locus_tag="P0D82_RS15910"
                     /old_locus_tag="P0D82_15905"
                     /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_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            3746..4054
                     /locus_tag="P0D82_RS15915"
                     /old_locus_tag="P0D82_15910"
     CDS             3746..4054
                     /locus_tag="P0D82_RS15915"
                     /old_locus_tag="P0D82_15910"
                     /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_002304909.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            4058..4420
                     /locus_tag="P0D82_RS15920"
                     /old_locus_tag="P0D82_15915"
     CDS             4058..4420
                     /locus_tag="P0D82_RS15920"
                     /old_locus_tag="P0D82_15915"
                     /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_002313294.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVGNELRADEKSAPSERNYPNESDGIFGGIPNRKSQ
                     MSESGFASMFSDVNSR"
                     /name="hypothetical protein"
     Typing          53..1455
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaaggttt acactctttt tattagcgac agcgcgaagg aggggtttaa cttggggttt
       61 agtatttcgt tcaaaaaggg aacaaagaat acaagcattt ctcataataa tcgtgagtta
      121 actgatagcc aaaaaatcaa tgactggcat aagcatattg atttcacaaa atcggatgaa
      181 aatatctatt tggaacaaat aaatattcgt gaaaaatatg aagaattatt cggtgaagcc
      241 gtagaaaaat ataatgcaaa gcagaaaaga gccgatagaa aaattgagga ctatttagca
      301 aaggttcgca aggataaaaa aatggaacca cagcgagaat ttatcgtgca aattggtact
      361 cttgatgatt ttcgtactac tcgtgatgat ggttcttcta ctggcatatc ggaacaacaa
      421 gcagaacaaa atcgagtgat tgccaacaaa attttagttg agtatttcaa agaatttaaa
      481 gaacggaatc ctagtttatc cgtctacaat gctgttattc ataatgacga agtaagtccg
      541 cacctgcatt tgaatattgt tcctgttgct gaagggtata aacggggtgt tcaaaagcaa
      601 ccaagtttta acaaagcctt gcaacagcag ggtttacgag cagataaaga gaatggtcga
      661 gtgatttgga ataattttag gaatcaggaa gttgagtcaa ttgaacgttt gatggcagat
      721 tttggttggg agcgtgagtt agtcggtact aacaaaatca aagatattca tgaatacaaa
      781 gaaatcatga gcgaaatttc cgaattgcgt caaacggccg taaaagagcg tgagagcgtt
      841 tctgatgagt tgaggtatat ttgtaggcaa agagaagaaa acgagcgtga gaaggctctg
      901 gtggcttctg agagagcgaa gattgaagaa gagaagaaaa atatgctgaa tgtaaaaaaa
      961 gagatggcgg tcattttcca aaaagatatg gttcctttag aaagtttcaa gaggcttcct
     1021 gatggttcgt atcatttatc tgggaatgat tttgttgatt tgtatcaacg agctacgaga
     1081 gcaacaaatg ccaagagaaa tgctgataac atgagtgagc aatatttaca gatgcttgag
     1141 caaaatacag aattaaatga gtatgtagct gcattggaag aagagcgtca tttgtctggt
     1201 agaaaacaat tagcagattt acaagtggaa aataaaaagc ttaaagaaga aaatcgctct
     1261 ttacgccagc gtttagagcg attaaaaaac gcatttcaaa aatcgatcac tcgtttgtct
     1321 atccgttttg ggcttgcaga aaaggatatg gggctttctg aggaattaga agtattagag
     1381 caggagaaaa ccttatttta tcgtcaaaac gtctcacagc ataaattaga gcgttctgaa
     1441 gatgagatcg agtggtagtt acgatgtgca gtcaacggta ccggaggcgg tttgtgccga
     1501 ggataaggag ttgacggcta aaccactagc ctattaagct gacatttgct aaaaaatggc
     1561 cagtccattt tttggccaac ttagcgttag cgaagtttgg gggcgccctt ttcaaagggt
     1621 gcggttttat gtttttggat atttgcatag ctaaagagaa gtgctattat tgagttatca
     1681 aataaataaa ctgaaaaaag agcaaaaaaa taaagtcgag caacgctgga cacgttctcg
     1741 acctttacgg aaactaatca cactagctcc gtaactcaaa ttcattatac gaataatttc
     1801 aggtttcttc aagactagag attgctggtt atgaattttt tagagttacg tgaactctgg
     1861 aaaattcttt ccaccaatct cttttttctt tgaggaggaa ctaaatttga gtaaaaaagg
     1921 cacgatcata aatgagtggg aaaaattaac agccccctct aacaggcggt taaatgtaaa
     1981 aactttttac acccccttaa aaatgcagtg gtcgattgat cgaattttat gtctttgggt
     2041 tttggggttt taaaacgaaa aaaagggggc gattttcgcc ctcttttttg atgttttttc
     2101 ttatcttgat actataggca actatttctg cgaagaaatc ggggctatag tatgggtcta
     2161 tcccttgtgg ctctaaggaa gaacaaaaaa aaagattgct ttttcttccc tagtatttta
     2221 tagttttaat tgactagaaa aaaactaaac tagaaaggag agcaatctat tttttgttat
     2281 cggcttttca gccttttttg tatacaaaat ttgtagattc agtatagcaa gatgaaaaag
     2341 aaaaagcaag atttgattaa cggaacattt cgagaaaaaa agaaaaattt gaaaaaagtg
     2401 gtggcattta gtgataatcg aatttctccc aaaatgcgtg aattgatgac aggctgtggt
     2461 tcatatttag aatttattgc aacgattgat aaggagaaaa agaaattggt ccaagctcac
     2521 ttttgtaaaa atcgtttctg tccgttatgt gcttggcgta aagctcgtaa ggattcgatg
     2581 atgttgtcga ttatgatgca agctattgcg gaagaaaagc agtatcaatt tatttttatg
     2641 acgttgacga caccgaatgt aaaagcggaa tgtttgaacg atgaaattga tttgtttaat
     2701 catgcattga aaaagatgtt tatgcgcaaa cgggttaaga cttcgattaa aggctatgtg
     2761 cgaaaattgg aaatcacgta caacaaaaaa cggaatgact ataacccgca ttttcacttg
     2821 attttggcag taaataaatc ttatttcacg gataaagatt attatatcaa gcaatcggaa
     2881 tggttagatt tgtggcggga agtgaccgga aaaacgggaa ttaatccgga tggtaccgac
     2941 gaaattaccc agttggatat tcgcaaggtc aaagggttcc aacaagaaaa agcagtacag
     3001 gaagttgcga aatattcggc aaaagatttt gaactgatcg aaagtcagga agtgtttgac
     3061 acattctatc atgcaatgaa aggtcgtcag ttgattacgt ttaacggtgt attcaaagaa
     3121 tacaagaaaa aatatgagtc gggtgacctt gatcgttata agaaaaaaga tgagaatgaa
     3181 tatttttggt ttttgactgc ttcgtggatg aggaaagaat cgaaatatgc ggttgattat
     3241 cgtgagatga gtgctgatga aagaaattat ttttcaggaa tgtatgtcga tgaaaaatct
     3301 gttgaggggg aaaatgaatg actgattcaa cggataaaat gacaattaag gcgcttgctg
     3361 atgaactagg aataaccaaa aatacagtga gaaattatct agtcaaagcc ggatatgatc
     3421 ttgctcggta caagaaaaat ggaattatct tgctagacaa agagttgatt ggtgttgctc
     3481 ggtcaattta tcggtcaaaa ggtggtcaat tgactggtca tttaccggtc aatagcacgg
     3541 gcagtgattt tcctttggaa aaagagaatg agtttttgcg tgatcaatta gctgagaagg
     3601 acaaacatat ttctgaatta acagaaatga ttcgtgatca acaaaaattg accctgcttc
     3661 agcaacaaaa aaacgatcag ttgttactag aaaatcaaga attaaaaaat cgaaaatggt
     3721 ggcaattctg gaagtgagat gtgacatgga taaaattgat ttgagagaag aaacagtcaa
     3781 tagaattgaa gtgatgtatg aacggttagc tgattatttg aatctttcgg atgaagataa
     3841 ttatagtgag atgcttgaac gaatgatgga tgttctcaac tcggttatca atgctgatct
     3901 agcaaaatct tcagttttga ctaatgaatt tgttcataag catttagcgc aaacaactga
     3961 tgaagctgaa aaagaatttt ggttgaaatt aatgagtcat attatgcagt taaaccaaat
     4021 ttccgttatt aattccaaag aaaaggggat gtagtttatg ggaatgactt tagcagatat
     4081 taaagtgcaa gaagaaaaat taaaaaaaga acaggcgaaa cttcgccaac agaagaaacg
     4141 attgattgag aaagaaaatg ctgcaatggg caaggctctt cgcaagcgtt ttgggtttga
     4201 atcttttgct gattttgagc ggtggctatc gtcgatttct gacgatcagc aacacgaaaa
     4261 atcagtgggt aatgagttgc gagctgatga aaaatcagca ccaagcgaac ggaattaccc
     4321 taacgaatct gacggaatat tcggagggat accgaataga aaaagtcaga tgagtgagag
     4381 tggatttgcg tcaatgttta gtgacgtaaa ttcacgataa gcgaatattt tgcatgaagc
     4441 aaaataaagc gtaaaaggag ttgagagcgt gacacgcttt cggctccttt tttcgttgtc
     4501 acttgtgacg gcgaaaaccc tcggagagcg tttggaattg tgacagtcat gtcacaatta
     4561 ggaaaacgtt actctttgac aaagagt
//
