LOCUS       NZ_CP092377             3782 bp    DNA     linear   CON 08-APR-2024
DEFINITION  Enterococcus faecium strain V13-21-E11-012-001 plasmid
            pK21EFM001_1_6, complete sequence.
ACCESSION   NZ_CP092377
VERSION     NZ_CP092377.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23500290
            Assembly: GCF_021172105.3
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3782)
  AUTHORS   Lim,S.-K., Moon,D.-C., Kim,S.-J., Yeom,Y.-J., Kang,Y.-J., Kim,Y.-J.
            and Baek,H.-J.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-FEB-2022) Bacterial Disease Division, Animal and Plant
            Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do
            39660, South Korea
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: CLC NGS Cell v. V.70
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 32.94x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021172105.3-RS_2024_04_08
            Annotation Date                   :: 04/08/2024 11:18:16
            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)                     :: 3,111
            CDSs (total)                      :: 3,022
            Genes (coding)                    :: 2,895
            CDSs (with protein)               :: 2,895
            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)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 42 of 127
            Pseudo Genes (incomplete)         :: 80 of 127
            Pseudo Genes (internal stop)      :: 25 of 127
            Pseudo Genes (multiple problems)  :: 16 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092377.1.
            Bacteria and source DNA available from Animal and Plant Quarantine
            Agency Bacterial Disease Division.
            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..3782
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="V13-21-E11-012-001"
                     /host="dog"
                     /db_xref="taxon:1352"
                     /plasmid="pK21EFM001_1_6"
                     /geo_loc_name="South Korea: Daegu"
                     /lat_lon="35.8303858 N 128.6299486 E"
                     /collection_date="2021-01-05"
     gene            626..1577
                     /locus_tag="LRL10_RS15415"
                     /old_locus_tag="LRL10_16195"
                     /pseudo=""
     CDS             626..1577
                     /locus_tag="LRL10_RS15415"
                     /old_locus_tag="LRL10_16195"
                     /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="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /name="RepB family plasmid replication initiator protein"
     gene            1598..2132
                     /locus_tag="LRL10_RS15420"
                     /old_locus_tag="LRL10_16200"
                     /pseudo=""
     CDS             1598..2132
                     /locus_tag="LRL10_RS15420"
                     /old_locus_tag="LRL10_16200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /name="DUF536 domain-containing protein"
     gene            2768..2992
                     /locus_tag="LRL10_RS15425"
                     /old_locus_tag="LRL10_16205"
     CDS             2768..2992
                     /locus_tag="LRL10_RS15425"
                     /old_locus_tag="LRL10_16205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363584.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="class II bacteriocin"
                     /protein_id="WP_002363584.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="class II bacteriocin"
     gene            3012..3299
                     /locus_tag="LRL10_RS15430"
                     /old_locus_tag="LRL10_16210"
     CDS             3012..3299
                     /locus_tag="LRL10_RS15430"
                     /old_locus_tag="LRL10_16210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_002363589.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     BGC             1..3782
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          628..1577
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.969"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccttacaaaa taaaatctgt gtggtgtttt taagtatccc ttattttcgg gttgttaggg
       61 cttgccctga ccgcctgtaa ggcgctttaa gaacaagata aggtttttta cccaagactg
      121 tcttaaaacg acttagacga gctatcagag gcttccccca cctccgttac tgacttgttt
      181 ttagcaaagg agcctttagg cgactgcgca gtacaatgtg agagcatagc gatcacactt
      241 ttttagcgac cgtagggagc aaggttttga attggcagtt ttgaaaaatg cgcgaacctg
      301 ttggtagaaa aaagaagtgg tttttttagg cgggaaattt tgtcaccctc ttttataatc
      361 tctttttaaa ccttttttta aacctcttta ccgtcggctg tgtccttact ccttcaatgg
      421 atacagcgtt ttataaacta cattttgtct gcttttaaac tacattttgt ctgcttttaa
      481 actacatttt gtctgctttt taaactacat tttgtctgct tttaaactct ttttttgcac
      541 tcacgtatgt tataatatgc attatcacag acaaaaacgt tgtttataac gtctgtatcc
      601 attgaaggag taaggaggaa tatctttggc aaatgaaatc gtgaaatacc atcatgaatt
      661 aaataccatt ccgttgcgga aatttacacc agttgaaatg aatctatttt tctctattgt
      721 gtctagaatg cgcgaaaaag gcgataaaac agtccgtctt acttttgacc aactaaaaga
      781 tttaagtaat tataaagcaa ctgctaataa tcgtttcatt aatgatttag aaatgactta
      841 tgataaatta atggatttac gttttggtaa aagaagtgct aatgggctcg atatagatag
      901 attcgttatg tttagtgagt ttaaaatacg tggaactgct aaagatccat atgtagacat
      961 acaagtttac gaaaaagctt tacctttact aaacaattta gatgagtggg ttcgctattc
     1021 actccaacaa tttaacgaat tacaaagtag ctatgcaaag actatgtttc gattactaaa
     1081 acaatatcga actaaaggtt ttgcttattt ttctaaagag gattttctat gaactattag
     1141 atattccaaa aagttactgg aacaaccaag caaacgttga taatcgtgtt ataaagccta
     1201 tacgacagga attaaccgca atcttcaaag gattatcaat caaaaagaaa tacggaaaag
     1261 ggcgaggaaa acctgtcgtt ggctatcaat ttacgtttaa accagaaatc aaaaaagcag
     1321 atgattttaa taaacatgca ccaaccaaag aagaacaaaa taaagcattg gctttagctg
     1381 ataaacaaaa agaatacgaa gaacctgcta caacaattaa cgaaaaaatc aaacagaaga
     1441 aacgagaact tgaactcctc caacaaatca aacaactaga aaaagagaaa gaagctcttg
     1501 aaaaacaaac agagtccgca ctttcgaaaa aagagaaaaa aagtttatta tctgatttag
     1561 ataatttatt ccagtagcaa cctaggaggc aaccagtatg caaccacaag aaacctttac
     1621 aataaaggaa ttgtcagaac ttttttaaga tgagtaggca agcaatatcg aaacatatcc
     1681 aaaaattaga ttcttccatg atagctaaaa atgagcgtgg ttataaggtt gtattgcgtt
     1741 ctggagtatt gcaacttgct cgcaacttag gcaaccaaat gttgctagat aggttgcacg
     1801 agtacgaaca agacaacgat aaaaatgtta atataccaag caaaaacgtg gttacaaaca
     1861 agttgctaga tcagttgcgt gaagaaaatg aatttttacg agaacaactt gccctcagag
     1921 agcaaaataa ttctcatata caaaaactac tcgaccagca acaacaactc accctacaag
     1981 ccaacaaaca aatcgaaaaa ctgcaagaaa aactacagtt gacttataca gaagaagctc
     2041 cagagaatga ctcaacgact ctttctgaag caacagaaac aatagacaaa caaattgata
     2101 ctgaaaaaaa atggtggcaa ctttggaaat aactggaggg aacattcatg acaagaaaaa
     2161 aatcttctat tcggttctat tttactagga attctaggat tcagtccgat gttattgtca
     2221 gtgatcaata aagggaataa acatggtgaa ttgaaattga atccaaatta ttacaacagt
     2281 cctaacgaag aattgtttgt aaaagaaaca gataaataat aaaaaagact gctctttcga
     2341 gcagccagtt aaaaaataat gagtgtttat tcttgaaaaa gcaacgcgct tatgaagcgc
     2401 taccaaaaat ttatcatatt ttattaaaaa taacaaccca gtaaaaaatg actggtaaaa
     2461 attcacaaag aaacggaaag aagcaaccgc agaaaatcaa gcttaaaaag agcttttgac
     2521 ctagaccaat cgaaaatcac aaagtgagcg cctgtatcta ttgctacagg cgctacttgg
     2581 catagtgtac attatgtcta ctagctgttt aaataactga tcttataatt ttatttaaac
     2641 gattatgaat tcaaaactac tttttatgac gttaatcatt gttatataat aaaatgttat
     2701 ataataaaat tactaagatt atttaatata acaagcaatt ttaaaaaaac gaaaaggaaa
     2761 aacaatcatg aaaaagaaag tattaaaaca ttgtgttatt ctaggaatat taggaacttg
     2821 tctagctggc atcggtacag gaataaaagt tgatgcagct acttactatg gaaatggtct
     2881 ttattgtaac aaagaaaaat gttgggtaga ttggaatcaa gctaaaggag aaattggaaa
     2941 aattattgtt aatggttggg ttaatcatgg tccatgggca cctagaaggt agtggtaggg
     3001 aggttattat aatggatttt actaaagaag aaaaactttt aaatgcaatt agtaaagtat
     3061 acaatgaagc aactatagat gactatcctg acttaaaaga aaagctcttt ctttattcta
     3121 aagaaatcag tgagggaaaa agtgttggtg aagttagtat gaaattaagt agttttcttg
     3181 gaagatatat tttaaaacat aaatttggat tacctaaatc tttaatagaa ttacaagaaa
     3241 ttgttagtaa ggaatctcaa gtatatagag gatgggcttc tattggtatt tggagttaat
     3301 tctttggaat aaaatgaaaa tgggactgaa gaatcaattc tgattcatca gtcccataaa
     3361 ttatagagcc gaaaaattat catatttata gatttattaa tagtaaatgg cataagaatc
     3421 tttgaacaac gaaaaaaatg tagctctacc taattattga tttgcaacaa tttcaccgaa
     3481 ggtgaaacaa gcgaaacttt acaaaaagtg gctagcattt gctagtcttt ttttgtattg
     3541 tggagagtgg gggggggagg gggattcaag ggggagcttg cgcccctttg acaagcggtt
     3601 atttgcacca aatacgtagg tatttggcta gcaaatatag agcttgccaa gccctttagt
     3661 aagctttagt gagctttact tattgtacct ttttaggtac aatggtattg cgaacgatac
     3721 gtccgtagga cgtactgaaa gggtgggact tatgagcgaa caaaatcaat atttggctag
     3781 ca
//
