LOCUS       NZ_CP131808             2947 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016N21-233 plasmid p2016N21-233-7,
            complete sequence.
ACCESSION   NZ_CP131808
VERSION     NZ_CP131808.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766204
            Assembly: GCF_038437885.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2947)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Rapid Diagnostics and Real-time Genomic Surveillance System for
            Pathogens from Culture
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2947)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2023) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, No. 35, Keyan
            Road, Zhunan Town, Miaoli County 350, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 28-SEP-2022
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038437885.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:04:14
            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)                     :: 3,196
            CDSs (total)                      :: 3,103
            Genes (coding)                    :: 2,933
            CDSs (with protein)               :: 2,933
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 63 of 170
            Pseudo Genes (incomplete)         :: 101 of 170
            Pseudo Genes (internal stop)      :: 39 of 170
            Pseudo Genes (multiple problems)  :: 31 of 170
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131808.1.
            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..2947
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016N21-233"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016N21-233-7"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(2775..2947,1..244)
                     /locus_tag="Q7583_RS15965"
                     /old_locus_tag="Q7583_15890"
     CDS             join(2775..2947,1..244)
                     /locus_tag="Q7583_RS15965"
                     /old_locus_tag="Q7583_15890"
                     /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_002322684.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIERNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGILIGTNSKVYQETKEKIEK
                     QLNPSKRNQPKNRQKETNQTFTSKNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(581..721)
                     /locus_tag="Q7583_RS15970"
                     /old_locus_tag="Q7583_15895"
     CDS             complement(581..721)
                     /locus_tag="Q7583_RS15970"
                     /old_locus_tag="Q7583_15895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002326822.1"
                     /GO_function="GO:0003700 - DNA-binding transcription factor
                     activity [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DeoR family transcriptional regulator"
                     /protein_id="WP_002322683.1"
                     /translation="MSDSIEKMTLKKLADELGVSKNTVRNQLVNSGFDLAQYKEKNAVV
                     N"
                     /name="DeoR family transcriptional regulator"
     gene            complement(718..1692)
                     /locus_tag="Q7583_RS15975"
                     /old_locus_tag="Q7583_15900"
     CDS             complement(718..1692)
                     /locus_tag="Q7583_RS15975"
                     /old_locus_tag="Q7583_15900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_002337993.1"
                     /translation="MSKRGTIINEWEKLNRISNRRLNAQTMCTPLKMQWSIDRITIVGT
                     LRENIYYHTPHDVLILDFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFQE
                     GKGRIDFNPNKISQFLAGSMKNFIHDLFLEPHFSRADIACDIIDVPDDFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKVVPKEIDTWWRLELQLRRG
                     KATDWHAMVHESLDSFASPHYLPEDVKVTDRMMITALITEHSYWGQIHRNSKYKYRELL
                     KQESQNDELTNHLRETFSESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2492..2773
                     /locus_tag="Q7583_RS15980"
                     /old_locus_tag="Q7583_15905"
     CDS             2492..2773
                     /locus_tag="Q7583_RS15980"
                     /old_locus_tag="Q7583_15905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347307.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347307.1"
                     /translation="MDILVRKIDSKVIAKIDKRCQELTNKTGKKWSRNRYLKVLIENDF
                     DHALMHYKKDQFDLLLEKFIAIQEKNTETLNEYVRTNNQLIETLIGGR"
                     /name="hypothetical protein"
     Typing          complement(722..1668)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.899"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 actaaatgct atgggaaaag aaatttccat catgtccgaa atcattgcag aatttgctga
       61 tttatatcta aaagatacag gtattcttat tggcacaaat tctaaagtgt atcaagaaac
      121 gaaagaaaaa attgaaaaac aacttaatcc ctccaaacga aatcaaccaa aaaatcgtca
      181 aaaagaaacc aatcaaacat ttacttctaa aaatttcgac ccaacaaatt ttctaaaaag
      241 ataaaaaata aaccaggaga tttaaattcc tggtttattt tttgggtagg atcaccatct
      301 taatagcaac atttacaata agatagtaac caattgaatg aaaaaaacga atttcagaag
      361 aaataacaga aaaaaagata aaaacaaaaa aattataaat acatgatttg aattcataat
      421 cgtaaaaaaa gctgctcgta cgagcagcta aataagaaaa agattggtat gttttaagga
      481 taaaataagt ataacaaatt tttcacatag agcaaagggg gcgaaaatcg cccccttttt
      541 ttcgttttaa aaccccaaaa cccaaagaca taaatttcgg tcaattgacc actgcatttt
      601 tttctttata ctgagcaagg tcaaatcccg aattgaccag ttgattgcgc accgtatttt
      661 tcgatacacc caattcatca gcaagttttt ttagggtcat tttttctatc gaatcactca
      721 ttcagcacct acttccgtca catcaagtcc ttgaagccat gtatctaatt ctcgtttcaa
      781 atcatctgcc gactccgaaa atgtttctcg caaatgattc gtcaactcat cattttgact
      841 ttcttgcttt aacaattcac gatatttata ttttgaattt ctatgaattt gcccccagta
      901 actatgttcc gttataagag cagtaatcat cattctgtca gttactttca catcttctgg
      961 caaatagtga ggacttgcaa agctatctaa actttcatga accattgcat gccaatcagt
     1021 tgctttcccc cttcgcaatt gcaattctag tcgccaccaa gtatcgattt ctttcggaac
     1081 aactttccgt tttctttctt gttccaattt tttgttatac atccgaatct gtcgttcact
     1141 agcacgactt ccccaatatg ctgtttccag tttcccagac cgaccgtaaa ttggtttgaa
     1201 agaaacagga tcaaccaccc gatattgggt aatgaaatca tctggcacgt caataatgtc
     1261 acaagcaata tctgcacgtg agaaatgtgg ttctaaaaat aaatcatgga taaagttctt
     1321 catcgagccc gccagaaatt ggctaatttt attggggtta aagtcaatcc gcccttttcc
     1381 ctcttgaaac ttaagaatct caatataagc tatattttcc tcatgttggt ctagtaattg
     1441 ccagccatta tttccaaccg cttttaaata tccgttacct tcgtttagac gcataagctg
     1501 ttcaaaatct aaaatcaaca catcatgggg agtgtgataa taaatatttt cccttaatgt
     1561 accaacaatg gtaattcggt caattgacca ttgcattttt aagggggtgc acatagtttg
     1621 tgcatttaac cgcctgttag atatgcggtt aagtttttcc cactcattta tgatcgtgcc
     1681 acgtttactc aaattttgtt cctcctcaaa gaaaaaagag atttttggaa agaatttcca
     1741 gagttcacgt aactctaaaa atccatatcc aaaaatctct agcttgaaga aacctaaaaa
     1801 tattcgtata atgaatttga gttacggaac taggtgagta gtttccgtaa ttagccgaag
     1861 ggtgcttcca acaccgttcg gcttttattt tgctcttttt tctcgttttc tttgattata
     1921 gcactcctct taaaaaaata aaaagacctc agggaatttc attccccgaa ccccttgagc
     1981 ctcctcctgc cgaaattatt tcacgcttcc gctcttcatt tcattcagtt ctcggcttgc
     2041 acaatctaac acgccgtttc gctaccagtc gccttacagg ctccattctc gcttctctta
     2101 cgtgttttaa cgattgtgcc gataactaaa cgaaatgaac gctaaaacgt cttagaacgc
     2161 aaaatacgcg cttataaaat catttcatct tgattacatg cccgtcataa tcgttcagtt
     2221 tagtttcatt ttcgtaaact ttttttattt ttacgaacag aaaaaagtcg cacatcacca
     2281 ttttataaag agcataagga aacgtgtacc cactttctaa aaaaagtggg tagataggct
     2341 gtgcctatca cgtttctcag aaaaaaattt gatatcactt tttcgccatc gtggctagct
     2401 tatgtatagt attttagcaa aaaacagcta tacaaatact atattcgtat gatatacata
     2461 aattatacac aaatgcgaaa ggagtttttc tatggacatt ttagttcgga agatcgattc
     2521 aaaggttatt gcaaaaatag acaaacgttg ccaagaactc acaaataaaa ctggcaaaaa
     2581 atggagtcga aatcgctact taaaagtcct aatcgaaaac gattttgacc acgcacttat
     2641 gcattacaag aaagatcaat tcgatttatt actcgaaaaa tttatcgcta ttcaagaaaa
     2701 aaatactgaa acgctgaatg aatatgttcg tacaaacaac caactcattg aaacacttat
     2761 cggaggaaga taacatgaga aaaacttctg ttcaaaaaca cgttaccctt tatcccagtc
     2821 acgtggacgt tttagattcc attatcgaaa gaaatccaga tatcaacaat tactcggaag
     2881 ccattcgttt tttatgtatg agttatgaac ctgataccaa tactacgact accagcaacc
     2941 aagccaa
//
