LOCUS       NZ_CP131840             2947 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S09-053 plasmid p2016S09-053-6,
            complete sequence.
ACCESSION   NZ_CP131840
VERSION     NZ_CP131840.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766200
            Assembly: GCF_038441115.1
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  JOURNAL   Unpublished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_038441115.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:54:39
            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)                     :: 3,177
            CDSs (total)                      :: 3,086
            Genes (coding)                    :: 2,953
            CDSs (with protein)               :: 2,953
            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)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 50 of 133
            Pseudo Genes (incomplete)         :: 74 of 133
            Pseudo Genes (internal stop)      :: 30 of 133
            Pseudo Genes (multiple problems)  :: 18 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131840.1.
            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="2016S09-053"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S09-053-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(200..340)
                     /locus_tag="Q7579_RS15870"
                     /old_locus_tag="Q7579_15810"
     CDS             complement(200..340)
                     /locus_tag="Q7579_RS15870"
                     /old_locus_tag="Q7579_15810"
                     /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(337..1311)
                     /locus_tag="Q7579_RS15875"
                     /old_locus_tag="Q7579_15815"
     CDS             complement(337..1311)
                     /locus_tag="Q7579_RS15875"
                     /old_locus_tag="Q7579_15815"
                     /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            2111..2392
                     /locus_tag="Q7579_RS15880"
                     /old_locus_tag="Q7579_15820"
     CDS             2111..2392
                     /locus_tag="Q7579_RS15880"
                     /old_locus_tag="Q7579_15820"
                     /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"
     gene            2394..2810
                     /locus_tag="Q7579_RS15885"
                     /old_locus_tag="Q7579_15825"
     CDS             2394..2810
                     /locus_tag="Q7579_RS15885"
                     /old_locus_tag="Q7579_15825"
                     /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"
     Typing          complement(341..1287)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.899"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaacaaaaaa attataaata catgatttga attcataatc gtaaaaaaag ctgctcgtac
       61 gagcagctaa ataagaaaaa gattggtatg ttttaaggat aaaataagta taacaaattt
      121 ttcacataga gcaaaggggg cgaaaatcgc cccctttttt tcgttttaaa accccaaaac
      181 ccaaagacat aaatttcggt caattgacca ctgcattttt ttctttatac tgagcaaggt
      241 caaatcccga attgaccagt tgattgcgca ccgtattttt cgatacaccc aattcatcag
      301 caagtttttt tagggtcatt ttttctatcg aatcactcat tcagcaccta cttccgtcac
      361 atcaagtcct tgaagccatg tatctaattc tcgtttcaaa tcatctgccg actccgaaaa
      421 tgtttctcgc aaatgattcg tcaactcatc attttgactt tcttgcttta acaattcacg
      481 atatttatat tttgaatttc tatgaatttg cccccagtaa ctatgttccg ttataagagc
      541 agtaatcatc attctgtcag ttactttcac atcttctggc aaatagtgag gacttgcaaa
      601 gctatctaaa ctttcatgaa ccattgcatg ccaatcagtt gctttccccc ttcgcaattg
      661 caattctagt cgccaccaag tatcgatttc tttcggaaca actttccgtt ttctttcttg
      721 ttccaatttt ttgttataca tccgaatctg tcgttcacta gcacgacttc cccaatatgc
      781 tgtttccagt ttcccagacc gaccgtaaat tggtttgaaa gaaacaggat caaccacccg
      841 atattgggta atgaaatcat ctggcacgtc aataatgtca caagcaatat ctgcacgtga
      901 gaaatgtggt tctaaaaata aatcatggat aaagttcttc atcgagcccg ccagaaattg
      961 gctaatttta ttggggttaa agtcaatccg cccttttccc tcttgaaact taagaatctc
     1021 aatataagct atattttcct catgttggtc tagtaattgc cagccattat ttccaaccgc
     1081 ttttaaatat ccgttacctt cgtttagacg cataagctgt tcaaaatcta aaatcaacac
     1141 atcatgggga gtgtgataat aaatattttc ccttaatgta ccaacaatgg taattcggtc
     1201 aattgaccat tgcattttta agggggtgca catagtttgt gcatttaacc gcctgttaga
     1261 tatgcggtta agtttttccc actcatttat gatcgtgcca cgtttactca aattttgttc
     1321 ctcctcaaag aaaaaagaga tttttggaaa gaatttccag agttcacgta actctaaaaa
     1381 tccatatcca aaaatctcta gcttgaagaa acctaaaaat attcgtataa tgaatttgag
     1441 ttacggaact aggtgagtag tttccgtaat tagccgaagg gtgcttccaa caccgttcgg
     1501 cttttatttt gctctttttt ctcgttttct ttgattatag cactcctctt aaaaaaataa
     1561 aaagacctca gggaatttca ttccccgaac cccttgagcc tcctcctgcc gaaattattt
     1621 cacgcttccg ctcttcattt cattcagttc tcggcttgca caatctaaca cgccgtttcg
     1681 ctaccagtcg ccttacaggc tccattctcg cttctcttac gtgttttaac gattgtgccg
     1741 ataactaaac gaaatgaacg ctaaaacgtc ttagaacgca aaatacgcgc ttataaaatc
     1801 atttcatctt gattacatgc ccgtcataat cgttcagttt agtttcattt tcgtaaactt
     1861 tttttatttt tacgaacaga aaaaagtcgc acatcaccat tttataaaga gcataaggaa
     1921 acgtgtaccc actttctaaa aaaagtgggt agataggctg tgcctatcac gtttctcaga
     1981 aaaaaatttg atatcacttt ttcgccatcg tggctagctt atgtatagta ttttagcaaa
     2041 aaacagctat acaaatacta tattcgtatg atatacataa attatacaca aatgcgaaag
     2101 gagtttttct atggacattt tagttcggaa gatcgattca aaggttattg caaaaataga
     2161 caaacgttgc caagaactca caaataaaac tggcaaaaaa tggagtcgaa atcgctactt
     2221 aaaagtccta atcgaaaacg attttgacca cgcacttatg cattacaaga aagatcaatt
     2281 cgatttatta ctcgaaaaat ttatcgctat tcaagaaaaa aatactgaaa cgctgaatga
     2341 atatgttcgt acaaacaacc aactcattga aacacttatc ggaggaagat aacatgagaa
     2401 aaacttctgt tcaaaaacac gttacccttt atcccagtca cgtggacgtt ttagattcca
     2461 ttatcgaaag aaatccagat atcaacaatt actcggaagc cattcgtttt ttatgtatga
     2521 gttatgaacc tgataccaat actacgacta ccagcaacca agccaaacta aatgctatgg
     2581 gaaaagaaat ttccatcatg tccgaaatca ttgcagaatt tgctgattta tatctaaaag
     2641 atacaggtat tcttattggc acaaattcta aagtgtatca agaaacgaaa gaaaaaattg
     2701 aaaaacaact taatccctcc aaacgaaatc aaccaaaaaa tcgtcaaaaa gaaaccaatc
     2761 aaacatttac ttctaaaaat ttcgacccaa caaattttct aaaaagataa aaaataaacc
     2821 aggagattta aattcctggt ttattttttg ggtaggatca ccatcttaat agcaacattt
     2881 acaataagat agtaaccaat tgaatgaaaa aaacgaattt cagaagaaat aacagaaaaa
     2941 aagataa
//
