LOCUS       NZ_CP083477             2056 bp    DNA     circular CON 04-NOV-2023
DEFINITION  Enterococcus faecium strain HJP554 plasmid pHJP554-4, complete
            sequence.
ACCESSION   NZ_CP083477
VERSION     NZ_CP083477.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21438094
            Assembly: GCF_020091325.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2056)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain HJP554
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2056)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-SEP-2021) State Key Laboratory of Pathogen and
            Biosecurity, Beijing Institute of Microbiology and Epidemiology,
            No.20,Dongdajie,Fengtai, Beijing, Beijing 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/04/2023 04:32:45
            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)                     :: 3,096
            CDSs (total)                      :: 3,006
            Genes (coding)                    :: 2,889
            CDSs (with protein)               :: 2,889
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 44 of 117
            Pseudo Genes (incomplete)         :: 66 of 117
            Pseudo Genes (internal stop)      :: 28 of 117
            Pseudo Genes (multiple problems)  :: 15 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083477.1.
            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..2056
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="HJP554"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHJP554-4"
                     /geo_loc_name="China:Shandong"
                     /lat_lon="36 N 120 E"
                     /collection_date="2020"
                     /collected_by="a teaching hospital"
     gene            309..464
                     /locus_tag="LA367_RS15425"
     CDS             309..464
                     /locus_tag="LA367_RS15425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299939.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CopG family transcriptional regulator"
                     /protein_id="WP_002299939.1"
                     /translation="MISNEKKRVVVTLTKEVADNLDKIAKQMGLSKSGLITIWVNANGK
                     ENEQKK"
                     /name="CopG family transcriptional regulator"
     gene            531..1133
                     /locus_tag="LA367_RS15430"
     CDS             531..1133
                     /locus_tag="LA367_RS15430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_010729575.1"
                     /translation="MTSRKTKDERTRNWTFVVYPESAPENWREFLDELHVPWVESPLHD
                     KDVNPDGELKKPHWHVLIMFSGKKTYDQIREITQKIRSPNPQKCANAKGMVRYFAHMDN
                     PEKFQYAKSDIIAHGGAEIASYLSVTSAERYELIREMMSFVDSKNITEIKDLIDYAMSE
                     RFDDWFPLLCDNSAYIIGQYIKSNRHGGSVNSKINKG"
                     /name="replication protein"
     gene            complement(1269..1526)
                     /locus_tag="LA367_RS15435"
     CDS             complement(1269..1526)
                     /locus_tag="LA367_RS15435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002377879.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002377879.1"
                     /translation="MPKETTINVEQLEKLLESYSNDFIELTGGKVEETTDLFDLLLTNI
                     LELNSEEQKEHKGKLIAPSYRKAAKSAVPTGFLTKQPYIF"
                     /name="hypothetical protein"
     gene            complement(1527..1748)
                     /locus_tag="LA367_RS15440"
     CDS             complement(1527..1748)
                     /locus_tag="LA367_RS15440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299940.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002299940.1"
                     /translation="MRVIKSEKFTLAEIMTTSELAQELDYNQAYVLRLAKEHLTEGKEY
                     RSAGRRNYLFSPEALKKLEKVITTKEGE"
                     /name="hypothetical protein"
     Typing          complement(1192..1367)
                     /name="MOBV"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.01e-87"
     Typing          532..1061
                     /name="rep_cluster_2351"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.812"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 cctgcatata tttcggtaga aggaggtcgg ggttcggggc ggagccctga ggtttgtttt
       61 ttggttttgg tgtttatgaa ttgggcggag gaggggggga ctacgacacc ccccttattg
      121 gtcattggtc attggtcgat agctgtttag ccttactctc ccaagggttt cagcgttttt
      181 ttttgacaaa atcagtaatg ccaagggttt aaggcctatt attcgctaat tagtatctaa
      241 actgttgcac cttagttact tttttgttac tatggttttt aagaaaaagt cgttggagga
      301 tacgaattat gatcagtaat gaaaaaaaga gagtcgttgt aacgcttact aaggaagtgg
      361 cagataatct tgataaaatt gcgaaacaaa tgggtcttag taagtctggt cttattacaa
      421 tttgggttaa tgctaacgga aaggaaaatg agcaaaaaaa atagcaaaag cattagtgtt
      481 ggcgcactgc ttttgctgtt agactgttgt tcaattaagg tgattatagc atgacgagta
      541 gaaaaactaa agatgaacgc acaaggaatt ggacgtttgt agtctatcct gaatcggctc
      601 ctgaaaattg gagggagttt ttagatgagt tacatgttcc ttgggttgag agtccacttc
      661 atgataaaga tgtgaatcct gacggtgaat tgaaaaagcc tcattggcat gttttgataa
      721 tgtttagcgg taaaaagacg tatgatcaaa tacgtgagat aactcaaaag attcggtctc
      781 caaacccgca aaaatgtgct aatgcaaaag gtatggtgcg atattttgct catatggata
      841 atccagaaaa atttcaatat gctaaaagtg atattatcgc tcatggtggt gcagaaattg
      901 ctagttattt gtcagtaacg agtgcagaac gatatgagtt gattagagag atgatgtcgt
      961 ttgttgattc taagaatatc actgaaatca aagatttaat tgactatgca atgtcagaaa
     1021 gatttgatga ttggtttccg cttctttgtg ataattcagc ttatattatc gggcaatata
     1081 taaaatcgaa tcgtcatggt ggaagtgtaa attcaaaaat aaataaagga taagagctgt
     1141 taatttcagc tctttttttg tgcgtgaaag tcttagtcac tatgaccaaa actacggacg
     1201 aaactatgac caaaagtagg tactatatta tgaccgaaaa taggtccaaa atggattttt
     1261 ttgtgatatc aaaaaatata aggttgtttt gtaagaaaac cagttggcac agccgactta
     1321 gccgccttcc tgtaggaagg tgctatcagt tttcccttat gctctttttg ttcttcagag
     1381 tttaattcca gaatatttgt gagaagtagg tcaaagaggt cggtggtttc ttcgactttt
     1441 ccgccggtca attcgataaa atcattggaa tatgattcta gcaatttttc tagttgttca
     1501 acgttgatag ttgtttcttt aggcatttac tcaccttctt tggtggttat gactttttct
     1561 agttttttaa gggcttctgg gctgaaaaga tagtttcttc taccggcaga gcgatattct
     1621 tttccttcag tcagatgttc tttcgctaag cgcaaaacgt aagcttggtt gtaatcaagt
     1681 tcttgtgcaa gttcgctggt cgtcataatt tcggccaaag tgaatttttc tgattttatc
     1741 actctcattt atgctccttc catttaacgt ccgtctatat tacgtgagta cgtcggactt
     1801 acgacataag cttataatat aagttttctg tgttgtggtc aattttatat tatcgaaatg
     1861 actagtagaa aaaatcaatg ctctaaaaag ggtctatttt gcgttttaag cgatttagcg
     1921 tctatttcgt ttagttatcg gcgcaatcgt taaaacacgt aagagaagcg agaatggagc
     1981 ctgtaaggcg actggtagcg aaacggtcgt gttagattgc aaaagccgat agctgaacga
     2041 aatagtaagc gtggcg
//
