LOCUS       NZ_CP083476             4952 bp    DNA     circular CON 04-NOV-2023
DEFINITION  Enterococcus faecium strain HJP554 plasmid pHJP554-3, complete
            sequence.
ACCESSION   NZ_CP083476
VERSION     NZ_CP083476.1
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 4952)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain HJP554
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4952)
  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
            CP083476.1.
            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..4952
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="HJP554"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHJP554-3"
                     /geo_loc_name="China:Shandong"
                     /lat_lon="36 N 120 E"
                     /collection_date="2020"
                     /collected_by="a teaching hospital"
     gene            254..1231
                     /locus_tag="LA367_RS15395"
     CDS             254..1231
                     /locus_tag="LA367_RS15395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /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="replication initiation protein"
                     /protein_id="WP_002338009.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIAYFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEEQNKALELVNQQIYSEKDPTSLQEKIKEQKRKLELLQQLEE
                     LERKQNNLNKENKEINEQIPDNNSDIPPELKKGLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            1241..1738
                     /locus_tag="LA367_RS15400"
     CDS             1241..1738
                     /locus_tag="LA367_RS15400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /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_002347002.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNIIYLKKEA
                     VTTITKVLSGNEPGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQLALETQQK
                     LLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQSKTEKKWWQF
                     WQ"
                     /name="DUF536 domain-containing protein"
     gene            2114..2395
                     /locus_tag="LA367_RS15405"
     CDS             2114..2395
                     /locus_tag="LA367_RS15405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353845.1"
                     /translation="MDILVRNINPKIITRIDKRCQELTTKTGKKWSRNQYLKILIENDF
                     DHELMNYKKDQFDLLFEKFIAIQAENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2397..2813
                     /locus_tag="LA367_RS15410"
     CDS             2397..2813
                     /locus_tag="LA367_RS15410"
                     /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_001232860.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PATNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            3467..4000
                     /locus_tag="LA367_RS15415"
     CDS             3467..4000
                     /locus_tag="LA367_RS15415"
                     /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            4012..4215
                     /locus_tag="LA367_RS15420"
     CDS             4012..4215
                     /locus_tag="LA367_RS15420"
                     /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"
     Typing          255..1231
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttataatct ctttttaaac ctctttttaa acctctttac cgtcggctgt atgcttactc
       61 tcccaaggtg tgcagaatct tttgggggtc tttttgtctg tttttagggg tctttttgtc
      121 tgtttttagg ggtctttttg tctgtttttg ggggtctttt tgtctgtttt taggggtctt
      181 taattagggg cttgacccct attagaaagc tctttataat tttgttaagt agttaatctt
      241 gaaggaggat tttatggcaa atgaaattgt gaaataccac catgaattaa atacgattcc
      301 tttacgcaaa tttacgtcag tagaaatgaa tttattcttc tctatagtat ctagaatgcg
      361 tgacgtaggc gataaaaaag tacaatttac attcgaacaa ttaaaagatt taagcaatta
      421 taaagcaact gcaaatgttc gattcataga tgatttagaa acaacgtatg acaaattaat
      481 ggatttacgt tttggtagaa gaagtgctga cggtttgcaa cgtgaacgat ttgttttatt
      541 taatcaattt aaaatcgatg gaaaagctga tattcctttt gctgaaatac aagtccatga
      601 gaaagcctta cccttactta ataatcttga agaatgggtt cgatattctc tccaacaatt
      661 caatgaatta gaaagcagtt attccaaaac catgtttaga ttattaaaac aatacagaac
      721 caaaggaatt gcctattttt caaaagaaga ctttcatgaa ttacttgata tccctaaaag
      781 ttatagagaa agtgatataa ataaaaaaat tataaagcct attcgccaag aactaaccgc
      841 aatcttcaaa ggtctgacaa tcaaaaagaa atacggaaaa ggaagaggaa aacctgtcat
      901 tggctatcaa ttcacgttta aacctgaaat aaaaaaagca gacgacttta ataaacacgc
      961 accaacaaaa gaagaacaaa ataaagcttt agaactagtt aatcaacaaa tttactctga
     1021 aaaagacccc acttcattac aagaaaaaat caaagaacag aaacgaaaat tagaactttt
     1081 acaacaatta gaagagctag aaagaaaaca aaataatctg aataaagaaa ataaggagat
     1141 taacgaacaa ataccagata acaattccga tattccccca gaattaaaaa aaggcttact
     1201 agataatctt caaaacttat ttaaagaata aggggttttt atgacagata aaactatcaa
     1261 agaattagca gatattctag gtgtttcaaa agataaagtg aagtatcaac tgaggaaatt
     1321 acctagtaat tttacctaca aaaaaggaaa tattatctac ctgaaaaaag aagcagtaac
     1381 aacaattaca aaggttttat caggtaatga gccgggtaac ttacctagtg aattacctga
     1441 ttcattacct accgattacc tactcaagga gattgaaact aagaataatc atattgaaga
     1501 aaaagatagg caaattgaaa aacttcaact agctttagaa acacaacaaa aattactcga
     1561 ccagcaacaa caactcaccc tgcaagccaa ccaacaaatc gagaaactgc aggaacaact
     1621 acagttgact tatacggaag aatcttcgga aaataaatca acgactcttt ctgaagaaac
     1681 agaatcgata gaaaaacaat caaagacgga gaaaaaatgg tggcaattct ggcaataaaa
     1741 ccagcaattt aaattaataa aaattgctgg ttttattctt ctttttgctt ttgcgagcag
     1801 agcaacatgg gcccatgttg cgatattttg gtggcgcccc aatccccgtt ttttcgttga
     1861 atcttactcg gactgcactc gttttacagc tgatttttct gaattttgaa agagcataag
     1921 gaaacgtggt atcactttct tacgaaaggt gctagataag ctgtgcctat cacgtttctc
     1981 agaaaaaaat ttgctatcac ttttttgcca ttgtggctag gctatgtata gtgttttggc
     2041 gaaaaatagc tatacaaata ctatatttgt atgatataca taaattatat actgatacga
     2101 aaggaaaatt tccatggaca ttttagttcg aaatatcaat cccaaaatta ttacaagaat
     2161 agataaacgt tgtcaggaac taacaaccaa aacgggcaaa aaatggagtc gaaatcaata
     2221 cctaaaaatt ttaatcgaaa acgattttga ccacgaactt atgaattaca aaaaagatca
     2281 attcgattta ttattcgaaa aatttattgc cattcaagca gaaaatacga acatactaaa
     2341 tgactatgtt cacacaaaca accaactcat tgaaacactt atcggaggaa tataacatga
     2401 gaaaaacttc tgttcaaaaa cacgtaaccc tttatcccag tcacgttgac gttttagatt
     2461 ccatcatcga aaaaaatcca gacgtcaaca attattcaga agccattcgc tttttatgta
     2521 tgagttatga acctgctacc aatacaacca caaccagtaa ccaagcaaaa ctcaatgcca
     2581 tgggaaaaga aatttctatc atgacagaaa tcatggcaga atttgctgat ttatatctaa
     2641 aagatactgg tgttcttatc ggtacaaatt ctaaagtata tcaagaagtg aaagaaaaaa
     2701 ttgaaaatca actcaatcct tcccgacgaa atcaacccaa aaatcgtcaa aaagaaacca
     2761 atcaaacctt tacttctgga aattttgacc caacaaactt tctaaaaaga taaaaaaaga
     2821 aaccgaaaaa taaaaaaatt cctcgatttc tttttaggga tcggtcttcc agcaagattt
     2881 gcaagttggt accaacttgc gaaaaaaaaa agaaaaatcc gcttctgcga attcttcttt
     2941 tttcattttg gggcgctgcc ctaatcccta agtcccggtt attcaatagc atggaaactc
     3001 aaagaataag acgttccctg gaataaaaaa aaggctgctc gttcgagcag tccatacata
     3061 ggaaaatgaa aaaacgacgt cccttactga gaaacgctat taaactttta acaaatcctc
     3121 taaaaaataa caagtcttta aaaagtgacc ggtaaaaatg cacaaagaac taaaaaagag
     3181 aaattgcatc aaatcaagca ttagaagcta gtaactagct agaccaattg aaaatcacaa
     3241 agtgagcgcc tgtatctatt gctacaggcg ctacttggca tagtgtacat tatgtcaaca
     3301 agaatttaat ataacatatt ttcctaatgc attctaacta taccacatta tcaaaaatat
     3361 aaattatctt tactaaataa aatattgaca agcctatacc ttttgtttta tgattttcac
     3421 aaagaaaacg ttttctatat atttttctgt atcaggagga aattctatga aaaaatttac
     3481 tttaggggta gctttgttaa ctattggggc agttgtttta ccgtcaacta ctatagttta
     3541 tgcttcagaa aattcccaag tggtatcatt aaacgaaaac aatgctactg aaaatgtagt
     3601 tattgagtac actgaagatg gtatggtcgt aactaaatat gaggatggtt atagtgcgga
     3661 agattttgca aattcttcag atatcatgac aagagctgca gttgcaagat ggggcaaaaa
     3721 ggaatataca aatattgctg taaccactgg agtagctgct aatgctatta atgctgcctt
     3781 ttgggcagga gggaaagcta gcacttctat gtttggtatc ccaggttggg caattggtgc
     3841 tttgttaaca ggtgcaagtt ggactaaaaa aggtgcttct ccagggaatg cagttgcaaa
     3901 agaatgggac aaaaatggta atggctggat tggattttat taccaaaggg gatatgatgc
     3961 agctggaaga gttgtagcta ctagatattc aacgttataa gttaaggagt gatgtttttg
     4021 atatctaaat cattaaaatc attaaaaaca tttactaaaa agaatccgca aatagctact
     4081 attcgtattt ttatatttgc tatagctgtt gctataattg ttaatatgct aagcggaggg
     4141 caattataca aatctggttt atttttagtg ttaatcttag ttgtcttaga cataataaag
     4201 tctaaaaaaa aataaatcga tacattttag aagaataggg ttgtttgaat attacaaagc
     4261 aacaatttca ccttcggtga aataagcgaa actttacaaa aagtggctag caaatgctag
     4321 ccttttttgt attgtagagc gtgaattttg agggggattc aagggggagc ttgcgcccct
     4381 ttgacaagcg gttatttgca ccaaatacct ccgtatttgg ctagcaatcc ttctaaaaaa
     4441 tacacctatc gatcagagtc aaaacaaatc aattttcgag tgagcgaatc cgaatttgca
     4501 aagctgaagc tttgcaaatg agtgtgccgg cttccgtaaa aatacatatg gctataattt
     4561 gcgttttaag gcgttttaaa cgttctggta tataattata ccaaaacaac tttaaaacgc
     4621 cttagatcta attttagagg tcttatagaa cattttaggg ttgttagggc ttgccctgac
     4681 cgcctgtaag gcgctttgag aacaagataa gggttttata ctaagactgt cttaaaacgg
     4741 cttaaacaaa cgctcagaac ttttcaaagg agttctttat gaactgtttt taagcaaagg
     4801 agcctttagg cgactgcgca gtataatgtg agagcgtagc gatcacacat ttttagtgac
     4861 cgtagggagc gagtttccca gtttagaaaa attcgcgaac ttgtttgagg aaaaaagcag
     4921 gagtttttta ggcgggaaat tttgcctcct ct
//
