LOCUS       NZ_CP114623             3960 bp    DNA     circular CON 15-FEB-2024
DEFINITION  Enterococcus faecium strain EF0656 plasmid pEF0656-6, complete
            sequence.
ACCESSION   NZ_CP114623
VERSION     NZ_CP114623.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32302292
            Assembly: GCF_027286245.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3960)
  AUTHORS   Luo,Q., Zhang,G. and Tian,W.
  TITLE     Complete genome sequence of Enterococcus faecium strain EF0656
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3960)
  AUTHORS   Luo,Q., Zhang,G. and Tian,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-DEC-2022) Zhuhai Hospital, Jinan University, 79
            Kangning Road, Zhuhai, Guangdong 519000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: HGAP v. 4; FALCON v. 0.3; Canu v. 0.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 58.82x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/15/2024 07:03:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,047
            CDSs (total)                      :: 2,955
            Genes (coding)                    :: 2,813
            CDSs (with protein)               :: 2,813
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 46 of 142
            Pseudo Genes (incomplete)         :: 91 of 142
            Pseudo Genes (internal stop)      :: 32 of 142
            Pseudo Genes (multiple problems)  :: 24 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP114623.1.
            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..3960
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="EF0656"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pEF0656-6"
                     /geo_loc_name="China: Zhuhai"
                     /lat_lon="22.22 N 113.55 E"
                     /collection_date="2022"
                     /collected_by="Wenfang Tian"
     gene            complement(132..1148)
                     /locus_tag="O4N81_RS15165"
                     /old_locus_tag="O4N81_15165"
     CDS             complement(132..1148)
                     /locus_tag="O4N81_RS15165"
                     /old_locus_tag="O4N81_15165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002326787.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVDDKV
                     HPLKLSWSIDRITIVGKLNDTIAYWTQNGVVFVDFEQLMRLNENQGYLKSVGTNGWQLF
                     DQYGEDIAYIEMLKFHPDKGRIDFNPNKIGEFLKGSMKQFIHDLFLDAHFSRADIACDI
                     LGVPDDFITQYRIVDPVSFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKQIV
                     PKEIETWWRIEMQLRRGKATDWHAMVRESLDSFASPHYLPGDVKPVDRIMIKGLNQDHS
                     EWAYISRNLKYRLRKLLKEESQNDELTNHLRETFKESANDLKIELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(2112..3128)
                     /locus_tag="O4N81_RS15170"
                     /old_locus_tag="O4N81_15170"
     CDS             complement(2112..3128)
                     /locus_tag="O4N81_RS15170"
                     /old_locus_tag="O4N81_15170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002326787.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVDDKV
                     HPLKLSWSIDRITIVGKLNDTIAYWTQNGVVFVDFEQLMRLNENQGYLKSVGTNGWQLF
                     DQYGEDIAYIEMLKFHPDKGRIDFNPNKIGEFLKGSMKQFIHDLFLDAHFSRADIACDI
                     LGVPDDFITQYRIVDPVSFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKQIV
                     PKEIETWWRIEMQLRRGKATDWHAMVRESLDSFASPHYLPGDVKPVDRIMIKGLNQDHS
                     EWAYISRNLKYRLRKLLKEESQNDELTNHLRETFKESANDLKIELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(133..899)
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2113..2879)
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaagcgtgtc acgctctcaa ctccttttac gctttatttt gcttcacgca aaataatcgc
       61 ttatcgtaaa ctcacgtcat taaacattga cgtaaattta ctctcactca tctgactttt
      121 cttattcggt atcacttctc tgtcacgtcc aaacccaaaa gccacgtgtc taattctatt
      181 ttcaagtcgt ttgcagattc cttaaacgtc tctcgtaaat gattcgtcaa ctcatcgttt
      241 tggctttctt ctttcaacaa tttgcgcaat ctatatttca aatttctgct aatatacgcc
      301 cactctgaat gatcttgatt cagccctttt atcataattc tatcaacagg ttttacatct
      361 ccaggcaagt aatgaggact tgcaaagcta tctaaacttt cccgaaccat cgcatgccaa
      421 tctgttgctt tgccacgtct tagctgcatt tctatacgcc accatgtttc gatttctttt
      481 ggtacaatct gtttttttcg ttcctgttca agctttttgt tgtacatccg cacttgtcgc
      541 tcgctggcac gactacccca gtacgctgtt tctaatttgc cagaacggcc ataaattggc
      601 ttaaaagaca cagggtcaac gattcgatac tgggtaataa aatcatcagg aacaccgaga
      661 atatcgcaag caatatctgc acgtgagaaa tgcgcatcca gaaacaaatc atgaatgaat
      721 tgtttcatcg acccctttaa aaactcgcca attttatttg gattaaaatc aatacgacct
      781 ttgtcagggt gaaattttaa catttcgata taggcgatat cttctccata ttggtcaaat
      841 aattgccaac catttgtacc aaccgacttc aaataccctt gattttcatt caaacgcatt
      901 aattgctcaa aatcgacaaa cacaactcca ttttgcgtcc aataagctat ggtatcattc
      961 agttttccga cgattgtaat tcgatcgatt gaccaactta attttagggg gtgtacctta
     1021 tcgtcaacac ttaaccgcct gttagaaata cggttaagtt tttcgagctg atttatcgtt
     1081 gttctttttt ctgcccctcg accttcaatt tttgattgaa tttcactcaa ctgattttca
     1141 tttgccattt tcgtcctcca gacgaaaaaa gagacttttg gaaagaattt ccagagttca
     1201 cgtaacccta aaaattcata tccaaaaatc tctagcttga agaaacctaa aaatattcgt
     1261 ataatgaacc tgagttacgg agctaggtga agtagtttcc gtaaatagtc gagagtgtta
     1321 gcgcactgct cggcttttat tttgctcttt tttctcgttt tctttgatta tagcactcct
     1381 cctaaaaaaa taaaaagacc tcagggaatt tcattccccg aaccccttga gcctcctcct
     1441 gccgaaatgg aaagggcgca cccgctgttt atttcattca gctatcggtt ttcacaatct
     1501 aacacgatcg ttccgctacc agtcgcctta caggctccat tttcgctcct ctaacgtgtt
     1561 ttaacgattg tgccgataac taaacgaaat aaacgctaaa accgctcaga acgcaaaata
     1621 tgccatttta gagctattgt agaaaatgta gtttgaaatg caattttctt ctttcagctt
     1681 tttatttccc acttgtaaat ctgctaatta ttttctacca gacaaaccat tgattttttg
     1741 gctatcagtt aactcacgat tattatgaga aatgcttgta ttctttgttc cctttttgaa
     1801 cgaaatacta aaccccaagt taaacccctc cttcgcgctg tcgctaataa aaagagtgta
     1861 aacctttctg ttactctttg acaaagagta aacattttcc taattgtgac atggctgtca
     1921 caattccaaa tgctctccga gggtattcgc tgtcacaagt gacaacgaaa aaaggagccg
     1981 aaagcgtgtc acgctctcaa ctccttttac gctttatttt gcttcacgca aaataatcgc
     2041 ttatcgtaaa ctcacgtcat taaacattga cgtaaattta ctctcactca tctgactttt
     2101 cttattcggt atcacttctc tgtcacgtcc aaacccaaaa gccacgtgtc taattctatt
     2161 ttcaagtcgt ttgcagattc cttaaacgtc tctcgtaaat gattcgtcaa ctcatcgttt
     2221 tggctttctt ctttcaacaa tttgcgcaat ctatatttca aatttctgct aatatacgcc
     2281 cactctgaat gatcttgatt cagccctttt atcataattc tatcaacagg ttttacatct
     2341 ccaggcaagt aatgaggact tgcaaagcta tctaaacttt cccgaaccat cgcatgccaa
     2401 tctgttgctt tgccacgtct tagctgcatt tctatacgcc accatgtttc gatttctttt
     2461 ggtacaatct gtttttttcg ttcctgttca agctttttgt tgtacatccg cacttgtcgc
     2521 tcgctggcac gactacccca gtacgctgtt tctaatttgc cagaacggcc ataaattggc
     2581 ttaaaagaca cagggtcaac gattcgatac tgggtaataa aatcatcagg aacaccgaga
     2641 atatcgcaag caatatctgc acgtgagaaa tgcgcatcca gaaacaaatc atgaatgaat
     2701 tgtttcatcg acccctttaa aaactcgcca attttatttg gattaaaatc aatacgacct
     2761 ttgtcagggt gaaattttaa catttcgata taggcgatat cttctccata ttggtcaaat
     2821 aattgccaac catttgtacc aaccgacttc aaataccctt gattttcatt caaacgcatt
     2881 aattgctcaa aatcgacaaa cacaactcca ttttgcgtcc aataagctat ggtatcattc
     2941 agttttccga cgattgtaat tcgatcgatt gaccaactta attttagggg gtgtacctta
     3001 tcgtcaacac ttaaccgcct gttagaaata cggttaagtt tttcgagctg atttatcgtt
     3061 gttctttttt ctgcccctcg accttcaatt tttgattgaa tttcactcaa ctgattttca
     3121 tttgccattt tcgtcctcca gacgaaaaaa gagacttttg gaaagaattt ccagagttca
     3181 cgtaacccta aaaattcata tccaaaaatc tctagcttga agaaacctaa aaatattcgt
     3241 ataatgaacc tgagttacgg agctaggtga agtagtttcc gtaaatagtc gagagtgtta
     3301 gcgcactgct cggcttttat tttgctcttt tttctcgttt tctttgatta tagcactcct
     3361 cctaaaaaaa taaaaagacc tcagggaatt tcattccccg aaccccttga gcctcctcct
     3421 gccgaaatgg aaagggcgca cccgctgttt atttcattca gctatcggtt ttcacaatct
     3481 aacacgatcg ttccgctacc agtcgcctta caggctccat tttcgctcct ctaacgtgtt
     3541 ttaacgattg tgccgataac taaacgaaat aaacgctaaa accgctcaga acgcaaaata
     3601 tgccatttta gagctattgt agaaaatgta gtttgaaatg caattttctt ctttcagctt
     3661 tttatttccc acttgtaaat ctgctaatta ttttctacca gacaaaccat tgattttttg
     3721 gctatcagtt aactcacgat tattatgaga aatgcttgta ttctttgttc cctttttgaa
     3781 cgaaatacta aaccccaagt taaacccctc cttcgcgctg tcgctaataa aaagagtgta
     3841 aacctttctg ttactctttg acaaagagta aacattttcc taattgtgac atggctgtca
     3901 caattccaaa tgctctccga gggtattcgc tgtcacaagt gacaacgaaa aaaggagccg
//
