LOCUS       NZ_CP131829             6303 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C07-254 plasmid p2016C07-254-4,
            complete sequence.
ACCESSION   NZ_CP131829
VERSION     NZ_CP131829.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766201
            Assembly: GCF_038441105.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6303)
  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  JOURNAL   Unpublished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 6303)
  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_038441105.1-RS_2024_04_25
            Annotation Date                   :: 04/25/2024 19:54:46
            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)                     :: 3,049
            CDSs (total)                      :: 2,960
            Genes (coding)                    :: 2,846
            CDSs (with protein)               :: 2,846
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 39 of 114
            Pseudo Genes (incomplete)         :: 61 of 114
            Pseudo Genes (internal stop)      :: 29 of 114
            Pseudo Genes (multiple problems)  :: 12 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131829.1.
            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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C07-254"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C07-254-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            1..951
                     /locus_tag="Q7580_RS15125"
                     /old_locus_tag="Q7580_15050"
     CDS             1..951
                     /locus_tag="Q7580_RS15125"
                     /old_locus_tag="Q7580_15050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /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="RepB family plasmid replication initiator
                     protein"
                     /protein_id="WP_342252027.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKKALEKQTESALSKKEKKSLLSDLDNLFQ"
                     /name="RepB family plasmid replication initiator protein"
     gene            972..1505
                     /locus_tag="Q7580_RS15130"
                     /old_locus_tag="Q7580_15055"
     CDS             972..1505
                     /locus_tag="Q7580_RS15130"
                     /old_locus_tag="Q7580_15055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /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_002321384.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1521..1691
                     /locus_tag="Q7580_RS15135"
                     /old_locus_tag="Q7580_15060"
     CDS             1521..1691
                     /locus_tag="Q7580_RS15135"
                     /old_locus_tag="Q7580_15060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            2141..2674
                     /locus_tag="Q7580_RS15140"
                     /old_locus_tag="Q7580_15065"
     CDS             2141..2674
                     /locus_tag="Q7580_RS15140"
                     /old_locus_tag="Q7580_15065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002334266.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     gene            2686..2889
                     /locus_tag="Q7580_RS15145"
                     /old_locus_tag="Q7580_15070"
     CDS             2686..2889
                     /locus_tag="Q7580_RS15145"
                     /old_locus_tag="Q7580_15070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002307460.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002321382.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            3211..3591
                     /locus_tag="Q7580_RS15150"
                     /old_locus_tag="Q7580_15075"
     CDS             3211..3591
                     /locus_tag="Q7580_RS15150"
                     /old_locus_tag="Q7580_15075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_002321381.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3573..4487
                     /locus_tag="Q7580_RS15155"
                     /old_locus_tag="Q7580_15080"
     CDS             3573..4487
                     /locus_tag="Q7580_RS15155"
                     /old_locus_tag="Q7580_15080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_342252026.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRT
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPNHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKTEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYTQFCDSLKTFGIHCLNRGKNFTYELVHKKKKVRS
                     NKLGKDYEKETILHELDRRERAYNQQRTNELRRARASIRETAEEVRREQRTFTPEQSEI
                     RPTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4732..5421
                     /locus_tag="Q7580_RS15160"
                     /old_locus_tag="Q7580_15085"
     CDS             4732..5421
                     /locus_tag="Q7580_RS15160"
                     /old_locus_tag="Q7580_15085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002321377.1"
                     /translation="MAFYLPYLLISASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLVG
                     VIFALSIVLSGLFGVLEGNKRVSRSILLGDITQKYEAACDKKKKEQALAQKMEEFTACY
                     EDMNNIFVDQEKRLTDKNMKKLTRFYQNLPEKQQKEVQEKYEQVKKDVQYFKDTQTEEA
                     CCNLFSDTIPFSTSEQERKERQQSVTYERYETLLQQATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     Typing          3..951
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.266"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3574..4484
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggcaaatg aaatcgtgaa ataccatcat gaattaaata ccattccgtt gcggaaattt
       61 acaccagttg aaatgaatct atttttctct attgtgtcta gaatgcgcga aaaaggcgat
      121 aaaacagtcc gtcttacttt tgaccaacta aaagatttaa gtaattataa agcaactgct
      181 aataatcgtt tcattaatga tttagaaatg acttatgata aattaatgga tttacgtttt
      241 ggtaaaagaa gtgctaatgg gctcgatata gatagattcg ttatgtttag tgagtttaaa
      301 atacgtggaa ctgctaaaga tccatatgta gacatacaag tttacgaaaa agctttacct
      361 ttactaaaca atttagatga gtgggttcgc tattcactcc aacaatttaa cgaattacaa
      421 agtagctatg caaagactat gtttcgatta ctaaaacaat atcgaactaa aggttttgct
      481 tatttttcta aagaggattt tcatgaacta ttagatattc caaaaagtta ctggaacaac
      541 caagcaaacg ttgataatcg tgttataaag cctatacgac aggaattaac cgcaatcttc
      601 aaaggattat caatcaaaaa gaaatacgga aaagggcgag gaaaacctgt cgttggctat
      661 caatttacgt ttaaaccaga aatcaaaaaa gcagatgatt ttaataaaca tgcaccaacc
      721 aaagaagacc aaaataaagc attggcttta gctgataaac aaaaagaata cgaagaaccc
      781 gctacaacaa ttaacgaaaa aatcaaacag aagaaacgag aacttgaact cctccaacaa
      841 atcaaacaac tagaaaaaga gaaaaaagct cttgaaaaac aaacagagtc cgcactttcg
      901 aaaaaagaga aaaaaagttt attatctgat ttagataatt tattccagta gcaacctagg
      961 aggcaaccag tatgcaacca caagaaacct ttacaataaa ggaattgtca gaacttttta
     1021 agatgagtag gcaagcaata tcgaaacata tccaaaaatt agattcttcc atgatagcta
     1081 aaaatgagcg tggttataag gttgtattgc gttctggagt attgcaactt gctcgcaact
     1141 taggcaacca aatgttgcta gataggttgc acgagtacga acaagacaac gataaaaatg
     1201 ttaatatacc aagcaaaaac gtggttacaa acaagttgct agatcagttg cgtgaagaaa
     1261 atgaattttt acgagaacaa cttgccctca gagagcaaaa taattctcat atacaaaaac
     1321 tactcgacca gcaacaacaa ctcaccctac aagccaacaa acaaatcgaa aaactgcaag
     1381 aaaaactaca gttgacttat acagaagaag ctccagagaa tgactcaacg actctttctg
     1441 aagcaacaga aacaatagac aaacaaattg atactgaaaa aaaatggtgg caactttgga
     1501 aataactgga gggaacattc atgacaagaa aaaatcttct attcggttct attttactag
     1561 gaattctagg attcagtccg atgttattgt cagtgatcaa taaagggaat aaacatggtg
     1621 aattgaaatt gaatccaaat tattacaaca gtcctaacga agaattgttt gtaaaagaaa
     1681 cagataaata ataaaaaaga ctgctctttc gagcagccag ttaaaaaata atgagtgttt
     1741 attcttgaaa aagcaacgcg cttatgaagc gctaccaaaa atttatcata ttttattaaa
     1801 aataacaacc cagtaaaaaa tgactggtaa aaattcacaa agaaacggaa agaagcaacc
     1861 gcagaaaatc aagcttaaaa agagcttttg acctagacca atcgaaaatc acaaagtgag
     1921 cctctgtatc ggttgataca agggctactt ggcatagtgt acattatgtc aacaagaatt
     1981 taatataaca tattttccta atgcattcta actataccac attatcaaaa atataaatta
     2041 tctttactaa ataaaatatt gacaagccta taccttttgt tttatgattt tcacaaagaa
     2101 aacgttttct atatattttt ctgtatcagg aggaaattct atgaaaaaat ttactttagg
     2161 ggtagctttg ttaactattg gggcagttgt tttaccgtca actactatag tttatgcttc
     2221 agaaaattcc caagtggtat cattaaacga aaacaatgct actgaaaatg tagttattga
     2281 gtacactgaa gatggtatgg tcgtaactaa atatgaggat ggttatagtg cggaagattt
     2341 tgcaaattct tcagatatca tgacaagagc tgcagttgca agatggggca aaaaggaata
     2401 tacaaatatt gctgtaacca ctggagtagc tgctaatgct attaatgctg ccttttgggc
     2461 aggagggaaa gctagcactt ctatgtttgg tatcccaggt tgggcaattg gtgctttgtt
     2521 aacaggtgca agttggacta aaaaaggtgc ttctccaggg aatgcagttg caaaagaatg
     2581 ggacaaaaat ggtaatggct ggattggatt ttattaccaa aggggatatg atgcagctgg
     2641 aagagttgta gctactagat attcaacgtt ataagttaag gagtgatgtt tttgatatct
     2701 aaatcattaa aatcattaaa aacatttact aaaaagaatc cgcaaatagc tactattcgt
     2761 atttttatat ttgctatagc tgttgctata attgttaata tgctaagcgg agggcaatta
     2821 tacaaatctg gtttattttt agtgttaatc ttagttgtct tagacataat aaagtctaaa
     2881 aaaaaataaa tcgatacatt ttagaagaat agggttgttt gaatattaca aagcaacaat
     2941 ttcaccttcg gtgaaataag cgaaacttta caaaaagtgg ctagcaaatg ctagcctttt
     3001 tttgtattgt ggagcgtgga ttttgagggg gattcaaggg ggagcttgcg ctcctttgac
     3061 aagcggttat ttgcaccaaa tacggaggta tttggctagc aaatatagag cttgccaaac
     3121 ccttttagtg agctttactc attgtacctt tttaggtaca atggtattgc gaacgatacg
     3181 tccgtaggac gtactgaaag ggtgggactt atgagcgaac aacatcaaaa tttggctagc
     3241 gatcattcta aaaaatatac ctatcgatcc gagccaaaac aaatcagttt tcgagtgagc
     3301 gaatccgaat ttgcaaagct gaagcagtca gctgaagctt tgcaaatgag tgtgccggct
     3361 ttcgtgaaag ccaaggcaca aaacgcgcgt ctggtgacac cgaaagtggc gccagacatt
     3421 gcccaggcaa tcgcgcgcga tttagccaaa gctggaggga atatcaatca aattgccaag
     3481 tggtgcaata cacaccaaca cgacgttgct cctgatgatg ctcaacgttt atccgaaaac
     3541 ctaaaaatca tgcaaaagga gctacaaaag atatggcaac agttaaagta agtcgaacca
     3601 cttcatgtag ccgagcaatc aattacgcag aaccacgagc aaccgtcaaa acaggaataa
     3661 actgtgacat tgattatgcc aaaagtgaaa tgaaacaaat acgcacgctt tatggaaaag
     3721 acgatcgtgt acaagcacac ttattgattc agtcctttcg accaggagaa attaccgctg
     3781 aaaaagccaa tcaactaggg gcagagtatg cgaaaaaaat agcccctaac caccaaatcg
     3841 cgatttacac acatacagac aaagaccata ttcataatca cattgtcatt aactccgtta
     3901 atcttgaaac tgggaaaaaa tttcaagccc atgggcaagc atttttaaac aaatgttatg
     3961 acctaaatga cgagatttgt cttgaacatg acttaacaat cacggaacga ggaaagaaaa
     4021 ccgaaaaacg aaccatgtct gaaattaaat taaaagaaaa aaatgaaccg gtttggaaag
     4081 acgaaattcg gtttgcgatt gatcaaacaa tgaaaaacaa aaaaactcga acgtataccc
     4141 aattttgtga ttcacttaaa acattcggca ttcattgctt gaatcgcgga aaaaatttta
     4201 cttacgaatt ggtccacaaa aagaaaaaag tacgatccaa caaactagga aaggattacg
     4261 aaaaggagac gattttacat gagctggaca gacgagaacg agcctacaat caacaacgaa
     4321 ccaacgagct acgaagagct cgagctagca ttcgcgaaac tgcagaagaa gtacgaagag
     4381 aacaacgaac ttttacgcct gaacaatcgg aaattagacc gactcgaaga aaccatgaac
     4441 aacacgttga acgaggaaca gaccaccaac aagaattatc gctctaaaac gttaaaagac
     4501 atcgaaaacg aaataaagag acaacgtgcc tttcttgcgc cttataccca agaaaggata
     4561 caaactacga tggattcaca agtcaaaaaa ctccaccaag cgctattaga ccagcgaaac
     4621 caagaacaaa aaaaggcttt aattcaacga tcgatggata ttcttgcccc cttatgttgc
     4681 ttagtactaa cattattagc cttttggttg gtatggggag aataaacaga catggcattc
     4741 tatttaccct atctactcat ttctgccagt attttaggaa ttatttggct tagctataag
     4801 gcttatcaaa caagatattc attaaaaggc tctaaaattc gatttaagcg atttttattg
     4861 gtcggggtta tatttgcctt atcaatcgtt ttaagtggtt tattcggcgt tttagagggt
     4921 aataaacgtg tttcaagaag cattttatta ggggatatca ctcaaaagta tgaagcagca
     4981 tgtgataaaa agaaaaaaga gcaagcatta gcacaaaaaa tggaggaatt taccgcttgt
     5041 tatgaggaca tgaacaatat ttttgtggat caagagaaac gtttaacaga taaaaacatg
     5101 aaaaaactca ctcgttttta tcaaaactta ccagaaaaac agcaaaaaga ggtacaagaa
     5161 aaatatgagc aagtaaaaaa agacgtgcaa tattttaaag atacgcagac agaagaagct
     5221 tgttgtaact tatttagcga tacaatccct ttttcaacca gtgaacaaga acgaaaagaa
     5281 cggcaacaat cggtcacata cgaacgttat gaaacactgc ttcagcaagc aacaaacata
     5341 caaaatccaa cgaaaaaaga aacggcatta aattatctag aaagtgtcaa ggaatggttg
     5401 gatcagcaac aacaaaattg aatttgatta gcaatcatgt taaactgaac ctgcaaatga
     5461 tcaaacatta gatacacgaa agccccagag aggtcggatt ctctggggct ttttttcagg
     5521 ttgatgtcgc ctttattgat tttacttctt gtttcggtta ttcaaccaat aactgaataa
     5581 agagacacaa acttctacaa gaagggggca aatgaaccgt tcaaacatta gatacacctc
     5641 cttccagtcg caagactgtc ggataggcga caagttatta taccttacaa aataaaatct
     5701 gtgtggtgtt tttaagtatc ccttattttc gggttgttag ggcttgccct gaccgcctgt
     5761 aaggcgcttt aagaacaaga taaggttttt tacccaagac tgtcttaaaa cgacttagac
     5821 gagctatcag aggcttcccc cacctccgtt actgacttgt ttttagcaaa ggagccttta
     5881 ggcgactgcg cagtacaatg tgagagcata gcgatcacac ttttttagcg accgtaggga
     5941 gcaaggtttt gaattggcag ttttgaaaaa tgcgcgaacc tgttggtaga aaaaagaagt
     6001 ggtttttagg cgggaaattt tgtcaccctc ttttataatc tctttttaaa ccttttttta
     6061 aacctcttta ccgtcggctg tgtccttact ccttcaatgg atacagcgtt ttataaacta
     6121 cattttgtct gcttttaaac tacattttgt ctgcttttaa actacatttt gtctgctttt
     6181 aaactacatt ttgtctgctt ttaaactctt tttttgcact cacgtatgtt ataatatgca
     6241 ttatcacaga caaaacgttg tttataacgt ctgtatccat tgaaggagta aggaggaata
     6301 tct
//
