LOCUS       NZ_CP119156             5807 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain GENOMIC22-005 plasmid pCFSAN126950_06,
            complete sequence.
ACCESSION   NZ_CP119156
VERSION     NZ_CP119156.1
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 5807)
  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  JOURNAL   Unpublished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 5807)
  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
            CP119156.1.
            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..5807
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-005"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1352"
                     /plasmid="pCFSAN126950_06"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            complement(join(5782..5807,1..940))
                     /locus_tag="P0D82_RS15830"
                     /old_locus_tag="P0D82_15825"
     CDS             complement(join(5782..5807,1..940))
                     /locus_tag="P0D82_RS15830"
                     /old_locus_tag="P0D82_15825"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="staphopain proregion domain-containing protein"
                     /protein_id="WP_275527625.1"
                     /translation="MKPKNKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPIEEQ
                     AINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDADNT
                     IKYVYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIKLLW
                     KSPLSTEKNGVSSFTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMINWR
                     IAETQTSFPWCAAYVEAAILCNKTDVRATSARAIMHYTYPNLNNSQIESKSLNQDQIIK
                     YANYCGVYPKKVARILNLSEVQTQLRKGNAIYRNCWLWKL"
                     /name="staphopain proregion domain-containing protein"
     gene            complement(1606..2022)
                     /locus_tag="P0D82_RS15835"
                     /old_locus_tag="P0D82_15830"
     CDS             complement(1606..2022)
                     /locus_tag="P0D82_RS15835"
                     /old_locus_tag="P0D82_15830"
                     /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_107538369.1"
                     /translation="MRKTSVQKHVTLYPSHIDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEK
                     QLNPSQRNQPKNRQKETSQTFTSKNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(2024..2305)
                     /locus_tag="P0D82_RS15840"
                     /old_locus_tag="P0D82_15835"
     CDS             complement(2024..2305)
                     /locus_tag="P0D82_RS15840"
                     /old_locus_tag="P0D82_15835"
                     /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_107532030.1"
                     /translation="MDILVRNINPKIITRVDKRCQELTTKTGEKWSRNKYLKVLIESDF
                     DRQLMNYKKEQFDLLLEKFIDIQTKNTETLNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            complement(2601..3116)
                     /locus_tag="P0D82_RS15845"
                     /old_locus_tag="P0D82_15840"
     CDS             complement(2601..3116)
                     /locus_tag="P0D82_RS15845"
                     /old_locus_tag="P0D82_15840"
                     /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_107532031.1"
                     /translation="MADKTIKDLAEELGVSKTAINKKVSDENRKLWFAKIGNKFVINEI
                     GQKAIKSMFFTENENSNQQPVGEKSKTENHKNANQVSELELFFFLEKQLNQKDIQLQEK
                     DEQLKQMQKLLDQQQQLTLQANQQIKKLHEQLQLTYAEESSEKEPLSVTEETQKGQNKE
                     KKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(3133..4065)
                     /locus_tag="P0D82_RS15850"
                     /old_locus_tag="P0D82_15845"
     CDS             complement(3133..4065)
                     /locus_tag="P0D82_RS15850"
                     /old_locus_tag="P0D82_15845"
                     /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_107532032.1"
                     /translation="MANEIVKYKPELNTIPLRKFTPIEMNLFFSIVSRMRDKGNQKIRF
                     YFDQLKDLSAYKQTAGEVFIKDLTRTYDHLMDLRFGKKSNGGLTIERFTMFTDFEIHGE
                     ADNPYVDIKVHEKALPLLNNLESWVRFSLTEFRDLNSSYAKTMFRLLKQYRTQGWAEFS
                     KEDFLELLDIPKSYRQTNINQFVLKPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTW
                     KAEINHADDFSKGKQEDLRTKLFNIEHNGELTQEEKWRAKDRILDLPLGTHEANFKKQQ
                     QTEKEEVEKQTLSNELKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            complement(<4743..4888)
                     /locus_tag="P0D82_RS15855"
                     /old_locus_tag="P0D82_15850"
                     /pseudo=""
     CDS             complement(<4743..4888)
                     /locus_tag="P0D82_RS15855"
                     /old_locus_tag="P0D82_15850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="frameshifted; internal stop; 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="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            complement(5188..5631)
                     /locus_tag="P0D82_RS15860"
                     /old_locus_tag="P0D82_15855"
     CDS             complement(5188..5631)
                     /locus_tag="P0D82_RS15860"
                     /old_locus_tag="P0D82_15855"
                     /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_233263658.1"
                     /translation="MGQYHYKLVNKPIVLVMGLVLVLFLTSCSKKQEIQKTELIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     Typing          complement(3136..4065)
                     /name="rep_cluster_1249"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.307"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tataaatggc atttcctttt cttagttgtg tttggacctc tgaaaggttt agtattcgtg
       61 ctactttttt aggataaaca ccacagtaat ttgcatattt tattatttga tcttgattaa
      121 gactttttga ttcaatttga ctgttgttta aattaggata ggtataatgc ataatggctc
      181 tagctgaagt agcgcgtaca tctgttttat tacataagat agcagcttct acgtaagcag
      241 cgcaccacgg aaaacttgtt tgggtttctg ctatacgcca attaatcata ataaagttat
      301 ctccggagga gacacttttt acacgtttaa ccgcaggaaa attttgtttt ttagagaaat
      361 ttttaatttt attttttata tttacggata taagatcatt tttttctgta aaggaagaga
      421 caccattttt ttctgtactt aaaggtgatt tccaaagtag tttaatttgg ccattatcgg
      481 aataataaat gctattatct tgaaaaaata aggttgtatc tgttatattg ctatctacta
      541 gattttgaag ttcttttgct aaaaattgtg aaatacttcc tgaatattct ccatttgtat
      601 tttttttgac ggtataaaca tatttaatcg tattatcagc gtctgaaaat actggaaaga
      661 aaatagaact atttgccgta ttttctccat cgagcatttt aaatggcgaa ccaagagtat
      721 agttaatatc agtttcagtg ttattttcca ttaaaagaat tgaagttatg gagtgttcaa
      781 aatcagtttt cgcaaaatta attgcttgtt cttcaattgg ttgggagttg atattgaaat
      841 tagaattttc tgaagcatag gtatttgtaa ttcctatact aaaaattcca atcatcaagg
      901 aaaagaggag acctagataa attttatttt tgggtttcaa aataatcacg cctttgtgtt
      961 aaaattaagt gatatacacc tataattaaa atatacaata tgcgataaca aatttttgtt
     1021 atagttcata aaatattgtt ttgggaacat aatcgttatt taacgagcta gttaacataa
     1081 tgtatactaa accaagtagc ccctctacca acggatacag gggcggactt tgtgattttt
     1141 cattggtcta gctaaaaaca actttctaaa gcttgatttt tcgcggttat ctgtgtccga
     1201 ttctttgtgc atttttatct gtcatttttt aaagacttgt tatttttatg agcgcttgtt
     1261 aaactataaa tacccttgtt ttttatcact tattttcatt atttaggtat tttattgtat
     1321 ttgtttgtgt tcgtgagtaa ttgcgtttgt tcgtttattt tttgcttgag actgctcttt
     1381 cgagcagtct ttttttttga ttgtttgcgt ataataaaaa agatcgttgc attcgcaaaa
     1441 tttgttacac ttattttacc cttaaaacaa gctgactttt tcttgtttag ctgctcgtac
     1501 gagcagcttt ttttttacgc aaattgggat cgatttgcaa atcttattgg aagaccgctc
     1561 tctagaaaat aaaccaggaa attaaaaatt tcctggttta tttttttatc tttttagaaa
     1621 gttggttggg tcgaaatttt tagaagtgaa tgtttgactc gtttcttttt gacgattctt
     1681 tggttgattt cgttgggagg gatttagctg tttttcaatt ttttctttta cttcttgata
     1741 tactttcgag tttgtaccga taagaacgcc tgtatctttt aaatacaaat cagcaaattc
     1801 tgcgataatt tcggtcatga tagaaatttc ttttcccatc gcatttagtt tggcttggtt
     1861 actggtagtt gttgtattgg tatcaggttc ataactcata cataaaaagc gaatggcttc
     1921 cgagtagtta ttgatatctg gatttttttc gatgatggaa tctaaaacgt caatgtgact
     1981 gggataaagg gtaacgtgtt tttgaacaga agtttttctc atgttatatt cctccgataa
     2041 gtgtttcaat gagttggttg tttgtatgaa catagtcgtt caatgtttca gtattttttg
     2101 tttgaatatc gataaatttt tcgagtaata aatcgaattg ctcttttttg taattcataa
     2161 gttgacggtc aaaatcactt tcgattagca cttttaaata tttatttcga ctccattttt
     2221 ctcctgtttt ggttgtaagt tcctgacaac gtttatctac tcttgtaata atttttggat
     2281 tgatatttcg aactaaaatg tccatagaaa acgtcctttc ttatgtgtgt ataatttatg
     2341 tatatcatac aaatatagta tttgtatagc tgttttttac cgaaatacta tacataagct
     2401 agccacaatg gcgaaaaagt gatagcaaat ttttttctta gaaacgtggt aggcacagcc
     2461 tacctagcac ctttcgtaag aaagtgatac cgcgtttcct tatgctcttt aaaaaatagc
     2521 gacgtgagat catgtcgcta tgcttgtaaa agcaaaaaaa gaaagtaacc caacaatttt
     2581 tatgaataaa aattgttggg ttattgccag aattgccacc attttttctc cttgttttgt
     2641 cctttttgag tttcttcagt aacagaaagg ggttcttttt ctgaagattc ttctgcatag
     2701 gttagctgga gttgttcgtg aagttttttg atttgttgat tggcttgtaa ggtgagttgt
     2761 tgttgctggt cgagtaattt ttgcatttgt tttaattgtt cgtctttttc ttgtagctgt
     2821 atatcttttt gatttaattg tttttctagg aaaaaaaaga gttctaattc ggaaacttgg
     2881 ttggcgtttt tatggttttc ggttttcgat ttttcgccaa ctggttgttg atttgagttt
     2941 tcgttttcgg taaaaaacat tgattttata gctttttgac cgatttcgtt aatcacaaac
     3001 ttgtttccga ttttcgcaaa ccaaagtttt cgattttcgt cagaaacttt tttgttaata
     3061 gctgtcttac taactcctaa ttcttcagca aggtctttga tcgttttatc tgccataaat
     3121 actccttata ctttaatcga ataagttttg taaatttcct aataaatctt gtttaagttc
     3181 gtttgaaagt gtttgttttt ccacttcttc tttttcagtt tgttgttgtt ttttaaaatt
     3241 agcttcatga gtacctaacg gaagatctag tattcgatct ttagcgcgcc atttttcttc
     3301 ttgcgttaat tctccattgt gttcaatatt aaataatttt gtacgtaaat cttcttgctt
     3361 cccttttgaa aaatcgtcag catgattaat ttcagctttc caagtaaaac gataaccaat
     3421 aacaggtttg cctcggcctt taccatattt tttacgaatc gttaatcctt taaataatgg
     3481 tgtgagttct tcttttatgg gtttgagtac aaactgattt atatttgttt gtctatagct
     3541 tttaggaata tctaatagtt ctaaaaaatc ttccttggaa aattcagccc atccttgtgt
     3601 tcggtattgt tttagtaatc taaacattgt tttagcataa ctgctattta aatctcgaaa
     3661 ttctgttaaa gagaaacgta cccaactttc taaattgtta agtaaaggca aagctttttc
     3721 gtgaactttt atatccacat aagggttatc ggcttctcca tgaatttcaa aatcagtaaa
     3781 cattgtaaat cgttctatgg ttaatccacc attgcttttt tttccaaaac gtaaatccat
     3841 taaatgatcg tatgttcttg ttaaatcttt tataaagact tctccagcag tttgcttata
     3901 agcacttaaa tctttaagct gatcgaaata aaagcgtatt ttttgattac ctttatcacg
     3961 cattctagaa acaatagaaa aaaacaagtt catttctatt ggagtaaatt tccttaaagg
     4021 aatggtattt aattctggtt tatattttac gatttcattt gccatttatt tgatactcca
     4081 gtctaactaa ttttattgac ataattttaa ggtatattat gtcttaaaac aatacctaaa
     4141 acagataatt tcatgcctat aaacagataa tttcatgcct ataaacagat aatttcatgc
     4201 ctataaacag ataatttcat gccctaaaaa agctacaggc cttgggagag taaggataca
     4261 gccgacggta aagaggttta aaaagaggtt ataaaagaga ttataaaaga ggggggcaaa
     4321 atttcccgcc taaaaatttc ctactttttt tctccaaaca ggttcgcgaa atttcctaaa
     4381 ctgggaatct gctccctacg gtcgctttaa aggtgtgatc gctacgctct cacattgaac
     4441 tgcgcagtcg cctaaaggct cctttgctta aaaacagttc gtaaggagtc ctttaagaag
     4501 ctctgagcgc tcatctacgg cgttttaaga caagtctaga taaaatccct tatcttgttt
     4561 ttaaagcgcc ttacaggcgg tcagggcaag ccctaacaac cctgaaacgt cctacaagac
     4621 ctataaaatt cgttttaagg cgttttaaag tcgctttggt ataaattaca taccagaacg
     4681 tttaaaacgc cttaaaacgc aaattagagc cttatgtata tatcgactaa tgttacctag
     4741 acttttacgg aagccggcac actcatttgc aaagcttcag atttgcaaat tcggattcgc
     4801 tcactcgaaa actgatttat tttgactctg atcaataggt gtatttttta gaaggattgc
     4861 tagccaaatt ttgctttaat ttgctcataa gtcccaccct tttgatacgt ccataggacg
     4921 tatcgtttgt aatgtgaaag tgactataag gtccctttct acaaaacaca ctaaagggtt
     4981 tggcaagctc tatatttgct agccaaatac cttcgtattt ggtgcaaata accgcttgtc
     5041 aaaggggaga aactccccct tgaatccccc tcaaaactca cgctccgcaa tacaaaaaag
     5101 gctagcaaat gctagccact ttttgtaaag tttcgcttgt ttcaccttcg gtgaaattat
     5161 tgttttgtaa tatcaaacaa ctattcatca atcagcttta aaaaattcaa ttggtttagc
     5221 tgtcccttct gtcccatcat tcgttgtcaa aataaatacg agcttttttg gagaatccaa
     5281 actaaaagtg taatctaatt gttttttatt agagcgcagt gttagtaaat tatttgttgc
     5341 tttgtaaatg aaaacttgtt catttatatt taaattttta tcaatgattt gaattttatg
     5401 attgttctct tttactaaga tggtatattg ttctatattt tttgaagtat ttaaattagt
     5461 gattactaga cgttctgagt gatctttagt ttgccaagtt cctagaaaag gaatcagctc
     5521 agtcttttgt atttcttgtt tttttgaaca actagttaag aaaagaacta acactagacc
     5581 cataactaaa acaatgggtt tatttaccaa tttgtaatgg tattgtccca agtaaaacca
     5641 cctccaggta caggaattgt aactggccct gcatttgcac ttattacagt tgggtagtta
     5701 taccaaggat tccacacata gtaagtttga taaccacctt gattgaccca cccaaataat
     5761 gcaagtgcat gacggctgtt actataattt ccataaccag cagttcc
//
