LOCUS       NZ_CP119157             4797 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain GENOMIC22-005 plasmid pCFSAN126950_07,
            complete sequence.
ACCESSION   NZ_CP119157
VERSION     NZ_CP119157.1
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 4797)
  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  JOURNAL   Unpublished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 4797)
  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
            CP119157.1.
            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..4797
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="GENOMIC22-005"
                     /isolation_source="EQA test strain"
                     /db_xref="taxon:1352"
                     /plasmid="pCFSAN126950_07"
                     /geo_loc_name="Denmark"
                     /collection_date="2022"
                     /collected_by="DTU National Food Institute"
     gene            join(4689..4797,1..317)
                     /gene="bacA"
                     /locus_tag="P0D82_RS15865"
                     /old_locus_tag="P0D82_15860"
     CDS             join(4689..4797,1..317)
                     /gene="bacA"
                     /locus_tag="P0D82_RS15865"
                     /old_locus_tag="P0D82_15860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002337995.1"
                     /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_002337995.1"
                     /translation="MICKNKKKIIAIIASFSLIFSTACTVLLTNNANVEAASSSYKHNH
                     AGYRCYKMSYYVSPSKCKQLARQTNKLNTVSAIANFIGLSGLTPGIISLVFGSAVSANN
                     VFVTAARRGKGVQLNYIAHFSNTTTYNYSSNQNYVIK"
                     /name="bacA"
     gene            347..511
                     /locus_tag="P0D82_RS15870"
                     /old_locus_tag="P0D82_15865"
     CDS             347..511
                     /locus_tag="P0D82_RS15870"
                     /old_locus_tag="P0D82_15865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334262.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002337996.1"
                     /translation="MKLTKIAVILAVIAGIILYFVLPANQFFLYFGIPAILIVNGVRIF
                     EQRKKCSST"
                     /name="hypothetical protein"
     gene            1469..2455
                     /locus_tag="P0D82_RS15875"
                     /old_locus_tag="P0D82_15870"
     CDS             1469..2455
                     /locus_tag="P0D82_RS15875"
                     /old_locus_tag="P0D82_15870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /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_275527626.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIAYFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEEQNKALELVNQQIYSEKDPTSLQEKIKEQKRKLELLQQLEE
                     LERKQNNLNKENKEINEQIPDNNSDIPPELVKLKKGLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            2465..2962
                     /locus_tag="P0D82_RS15880"
                     /old_locus_tag="P0D82_15875"
     CDS             2465..2962
                     /locus_tag="P0D82_RS15880"
                     /old_locus_tag="P0D82_15875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /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_002347002.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNIIYLKKEA
                     VTTITKVLSGNEPGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQLALETQQK
                     LLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQSKTEKKWWQF
                     WQ"
                     /name="DUF536 domain-containing protein"
     gene            3338..3619
                     /locus_tag="P0D82_RS15885"
                     /old_locus_tag="P0D82_15880"
     CDS             3338..3619
                     /locus_tag="P0D82_RS15885"
                     /old_locus_tag="P0D82_15880"
                     /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_000353845.1"
                     /translation="MDILVRNINPKIITRIDKRCQELTTKTGKKWSRNQYLKILIENDF
                     DHELMNYKKDQFDLLFEKFIAIQAENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            3621..4037
                     /locus_tag="P0D82_RS15890"
                     /old_locus_tag="P0D82_15885"
     CDS             3621..4037
                     /locus_tag="P0D82_RS15890"
                     /old_locus_tag="P0D82_15885"
                     /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_001232860.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PATNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     Typing          1470..2455
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.088"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caagctcttc ttacaaacat aatcatgctg gttatagatg ttacaaaatg agttattatg
       61 taagtccttc taaatgcaaa caattggctc gccaaactaa taaacttaat accgtctcag
      121 ctattgcaaa ctttattgga ctatctggat taacaccggg gattatatca ttagttttcg
      181 gatcagcagt tagtgctaat aatgtatttg ttacagccgc tagaagagga aaaggcgttc
      241 aattaaatta tattgcccat tttagtaata ccactaccta taattatagt tctaaccaaa
      301 attatgttat aaaataatta aaactttaaa ctaggaggaa tgctttatga aattaacaaa
      361 aattgctgta attttagctg ttattgctgg cattatttta tattttgtat tgcctgctaa
      421 tcaattcttc ctttactttg gaatacctgc gattttaata gtaaatggcg taagaatctt
      481 tgaacaacga aaaaaatgta gctctaccta atcgttacaa aacaacaatt tcaccttcgg
      541 tgaaataagc gaaactttac aaaaagtggc tagcaaatgc tagccttttt tgtattgtag
      601 agcgtgaatt ttgaggggga ttcaaggggg agcttgcgcc cctttgacaa gcggttattt
      661 gcaccaaata cctccgtatt tggctagcaa tccttctaaa aaatacacct atcgatcaga
      721 gtcaaaacaa atcaattttc gagtgagcga atccgaattt gcaaagctga agctttgcaa
      781 atgagtgtgc cggcttccgt aaaaatacat atggctataa tttgcgtttt aaggcgtttt
      841 aaacgttctg gtatataatt ataccaaaac aactttaaaa cgccttagat ctaattttag
      901 aggtcttata gaacatttta gggttgttag ggcttgccct gaccgcctgt aaggcgcttt
      961 gagaacaaga taagggtttt atactaagac tgtcttaaaa cggcttaaac aaacgctcag
     1021 aacttttcaa aggagttctt tatgaactgt ttttaagcaa aggagccttt aggcgactgc
     1081 gcagtataat gtgagagcgt agcgatcaca catttttagt gaccgtaggg agcgagtttc
     1141 ccagtttaga aaaattcgcg aacttgtttg aggaaaaaag caggagtttt ttaggcggga
     1201 aattttgcct cctcttttat aatctctttt taaacctctt tttaaacctc tttaccgtcg
     1261 gctgtatgct tactctccca aggtgtgcag aatcttttgg gggtcttttt gtctgttttt
     1321 aggggtcttt ttgtctgttt ttaggggtct ttttgtctgt ttttgggggt ctttttgtct
     1381 gtttttaggg gtctttaatt aggggcttga cccctattag aaagctcttt ataattttgt
     1441 taagtagtta atcttgaagg aggattttat ggcaaatgaa attgtgaaat accaccatga
     1501 attaaatacg attcctttac gcaaatttac gtcagtagaa atgaatttat tcttctctat
     1561 agtatctaga atgcgtgacg taggcgataa aaaagtacaa tttacattcg aacaattaaa
     1621 agatttaagc aattataaag caactgcaaa tgttcgattc atagatgatt tagaaacaac
     1681 gtatgacaaa ttaatggatt tacgttttgg tagaagaagt gctgacggtt tgcaacgtga
     1741 acgatttgtt ttatttaatc aatttaaaat cgatggaaaa gctgatattc cttttgctga
     1801 aatacaagtc catgagaaag ccttaccctt acttaataat cttgaagaat gggttcgata
     1861 ttctctccaa caattcaatg aattagaaag cagttattcc aaaaccatgt ttagattatt
     1921 aaaacaatac agaaccaaag gaattgccta tttttcaaaa gaagactttc atgaattact
     1981 tgatatccct aaaagttata gagaaagtga tataaataaa aaaattataa agcctattcg
     2041 ccaagaacta accgcaatct tcaaaggtct gacaatcaaa aagaaatacg gaaaaggaag
     2101 aggaaaacct gtcattggct atcaattcac gtttaaacct gaaataaaaa aagcagacga
     2161 ctttaataaa cacgcaccaa caaaagaaga acaaaataaa gctttagaac tagttaatca
     2221 acaaatttac tctgaaaaag accccacttc attacaagaa aaaatcaaag aacagaaacg
     2281 aaaattagaa cttttacaac aattagaaga gctagaaaga aaacaaaata atctgaataa
     2341 agaaaataag gagattaacg aacaaatacc agataacaat tccgatattc ccccagaatt
     2401 agtaaaatta aaaaaaggct tactagataa tcttcaaaac ttatttaaag aataaggggt
     2461 ttttatgaca gataaaacta tcaaagaatt agcagatatt ctaggtgttt caaaagataa
     2521 agtgaagtat caactgagga aattacctag taattttacc tacaaaaaag gaaatattat
     2581 ctacctgaaa aaagaagcag taacaacaat tacaaaggtt ttatcaggta atgagccggg
     2641 taacttacct agtgaattac ctgattcatt acctaccgat tacctactca aggagattga
     2701 aactaagaat aatcatattg aagaaaaaga taggcaaatt gaaaaacttc aactagcttt
     2761 agaaacacaa caaaaattac tcgaccagca acaacaactc accctgcaag ccaaccaaca
     2821 aatcgagaaa ctgcaggaac aactacagtt gacttatacg gaagaatctt cggaaaataa
     2881 atcaacgact ctttctgaag aaacagaatc gatagaaaaa caatcaaaga cggagaaaaa
     2941 atggtggcaa ttctggcaat aaaaccagca atttaaatta ataaaaattg ctggttttat
     3001 tcttcttttt gcttttgcga gcagagcaac atgggcccat gttgcgatat tttggtggcg
     3061 ccccaatccc cgttttttcg ttgaatctta ctcggactgc actcgtttta cagctgattt
     3121 ttctgaattt tgaaagagca taaggaaacg tggtatcact ttcttacgaa aggtgctaga
     3181 taagctgtgc ctatcacgtt tctcagaaaa aaatttgcta tcactttttt gccattgtgg
     3241 ctaggctatg tatagtgttt tggcgaaaaa tagctataca aatactatat ttgtatgata
     3301 tacataaatt atatactgat acgaaaggaa aatttccatg gacattttag ttcgaaatat
     3361 caatcccaaa attattacaa gaatagataa acgttgtcag gaactaacaa ccaaaacggg
     3421 caaaaaatgg agtcgaaatc aatacctaaa aattttaatc gaaaacgatt ttgaccacga
     3481 acttatgaat tacaaaaaag atcaattcga tttattattc gaaaaattta ttgccattca
     3541 agcagaaaat acgaacatac taaatgacta tgttcacaca aacaaccaac tcattgaaac
     3601 acttatcgga ggaatataac atgagaaaaa cttctgttca aaaacacgta accctttatc
     3661 ccagtcacgt tgacgtttta gattccatca tcgaaaaaaa tccagacgtc aacaattatt
     3721 cagaagccat tcgcttttta tgtatgagtt atgaacctgc taccaataca accacaacca
     3781 gtaaccaagc aaaactcaat gccatgggaa aagaaatttc tatcatgaca gaaatcatgg
     3841 cagaatttgc tgatttatat ctaaaagata ctggtgttct tatcggtaca aattctaaag
     3901 tatatcaaga agtgaaagaa aaaattgaaa atcaactcaa tccttcccga cgaaatcaac
     3961 ccaaaaatcg tcaaaaagaa accaatcaaa cctttacttc tggaaatttt gacccaacaa
     4021 actttctaaa aagataaaaa aagaaaccga aaaataaaaa aattcctcga tttcttttta
     4081 gggatcggtc ttccagcaag atttgcaagt tggtaccaac ttgcgaaaaa aaaaagaaaa
     4141 atccgcttct gcgaattctt cttttttcat tttggggcgc tgccctaatc cctaagtccc
     4201 ggttattcaa tagcatggaa actcaaagaa taagacgttc cctggaataa aaaaaaggct
     4261 gctcgttcga gcagtccata cataggaaaa tgaaaaaacg acgtccctta ctgagaaacg
     4321 ctattaaact tttaacaaat cctctaaaaa ataacaagtc tttaaaaagt gaccggtaaa
     4381 aatgcacaaa gaactaaaaa agagaaattg catcaaatca agcattagaa gctagtaact
     4441 agctagacca attgaaaatc acaaagtgag cgcctgtatc tattgctaca ggcgctactt
     4501 ggcatagtgt acattatgtc aacaagaatt taatataaca tatttttcta gtttgttata
     4561 acaatgccac tctaacaaaa atgtaagcat tatccttatt aaaagctcct tgacaaggac
     4621 tatacctttt attttatgat ttttacatag aaaacgtttt ctctattttt tgtttagagg
     4681 tgatttttat gatttgcaag aacaagaaaa aaattattgc tattattgct agtttctctt
     4741 tgatttttag tactgcatgt actgtcttat taacaaataa tgctaatgtt gaagctg
//
