LOCUS       NZ_CP084439             2415 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Staphylococcus lugdunensis strain RMLUG3 plasmid pRMLUG3_2, complete
            sequence.
ACCESSION   NZ_CP084439
VERSION     NZ_CP084439.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21459166
            Assembly: GCF_026427475.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus lugdunensis
  ORGANISM  Staphylococcus lugdunensis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2415)
  AUTHORS   Fu,S.
  TITLE     The complete genome sequence of Staphylococcus lugdunensis shows the
            characteristics of the staphylococcal cassette chromosome mec and
            lugdunin operon
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2415)
  AUTHORS   Fu,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2021) Department of Respiratory and Critical Care
            Medicine, Peking University People's Hospital, No.11 Xizhimen South
            Street, Xicheng District, Beijing, Beijing 100044, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 541.1x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_026427475.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 06:43:54
            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)                     :: 2,482
            CDSs (total)                      :: 2,402
            Genes (coding)                    :: 2,371
            CDSs (with protein)               :: 2,371
            Genes (RNA)                       :: 80
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 31
            CDSs (without protein)            :: 31
            Pseudo Genes (ambiguous residues) :: 0 of 31
            Pseudo Genes (frameshifted)       :: 9 of 31
            Pseudo Genes (incomplete)         :: 23 of 31
            Pseudo Genes (internal stop)      :: 6 of 31
            Pseudo Genes (multiple problems)  :: 7 of 31
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084439.1.
            Bacteria and source DNA available from homo sapiens.
            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..2415
                     /organism="Staphylococcus lugdunensis"
                     /mol_type="genomic DNA"
                     /strain="RMLUG3"
                     /isolation_source="wound secretion"
                     /host="Homo sapiens"
                     /db_xref="taxon:28035"
                     /plasmid="pRMLUG3_2"
                     /geo_loc_name="China:Fujian"
                     /collection_date="2017-08-17"
     gene            join(2121..2415,1..182)
                     /locus_tag="LE166_RS12405"
                     /old_locus_tag="LE166_12410"
     CDS             join(2121..2415,1..182)
                     /locus_tag="LE166_RS12405"
                     /old_locus_tag="LE166_12410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            939..1673
                     /gene="erm(C)"
                     /locus_tag="LE166_RS12410"
                     /old_locus_tag="LE166_12415"
     ARG             940..1670
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             940..1673
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          2..192
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.969"
                     /coverage="100.0"
                     /evalue="1.72e-92"
ORIGIN
        1 tcttagaaga aggaaatatt ataaaaagaa aaactggagt attaatgtta aaccctgaac
       61 tactaatgag aggcgacgac caaaaacaaa aatacctctt actcgaattt gggaactttg
      121 agcaagaggc aaatgaaaaa caagaaaatg cattatctga ttattattct ttcaaggact
      181 agtataacat aaaatcgtct acaaatagac aaaaaacctg cacgcttaat gtaaatcaaa
      241 agcttaacgc aaatgaaata gattgacctc ccaataacac cacgtagtta ttgggaggtc
      301 aatctatgaa atgcgattaa gctttttcta attcacataa gcgtgcaggt ttaaagtaca
      361 taaaaaatat aatgaaaaaa agcatcatta tactaacgtt ataccaacat tatactctca
      421 ttatactaat tgcttattcc aatttcctat tggttggaac caacaggcgt tagtgtgttg
      481 ttgagttggt actttcatgg gattaatccc atgaaacccc caaccaactc gccaaagctt
      541 tggctaacac acacgccatt ccaaccaata gttttctcgg cataaagcca tgctctgacg
      601 cttaaatgca ctaatacctt aaaaaaacat taaagtctaa cacactagac ttatttactt
      661 cgtaattaag tcgttaaacc gtgtgctcta cgaccaaaag tataaaacct ttaagaactt
      721 tcttttttct tgtaaaaaaa gaaactagat aaatctctca tatcttttat tcaataatcg
      781 catcagattg cagtataaat ttaacgatca ctcatcatgt tcatatttat cagagctcgt
      841 gctataatta tactaatttt ataaggagga aaaaataagt ggttataatg aatcgttaat
      901 aagcaaaatt cattataacc aaattaaaga gggttataat gaacgagaaa aatataaaac
      961 acagtcaaaa ctttattact tcaaaacata atatagataa aataatgaca aatataagat
     1021 taaatgaaca tgataatatc tttgaaatcg gctcaggaaa agggcatttt acccttgaat
     1081 tagtacagag gtgtaatttc gtaactgcca ttgaaataga ccataaatta tgcaaaacta
     1141 cagaaaataa acttgttgat cacgataatt tccaagtttt aaacaaggat atattgcagt
     1201 ttaaatttcc taaaaaccaa tcctataaaa tatttggtaa tataccttat aacataagta
     1261 cggatataat acgcaaaatt gtttttgata gtatagctga tgagatttat ttaatcgtgg
     1321 aatacgggtt tgctaaaaga ttattaaata caaaacgctc attggcatta tttttaatgg
     1381 cagaagttga tatttctata ttaagtatgg ttccaagaga atattttcat cctaaaccta
     1441 aagtgaatag ctcacttatc agattaaata gaaaaaaatc aagaatatca cacaaagata
     1501 aacagaagta taattatttc gttatgaaat gggttaacaa agaatacaag aaaatattta
     1561 caaaaaatca atttaacaat tccttaaaac atgcaggaat tgacgattta aacaatatta
     1621 gctttgaaca attcttatct cttttcaata gctataaatt atttaataag taagttaagg
     1681 gatgcataaa ctgcatccct taacttgttt ttcgtgtacc tattttttgt gaatcgatta
     1741 tgtcttttgc gcattcactt cttttctata taaatatgag cgaagcgaat aagcgtcgga
     1801 aaagcagcaa aaagtttcct ttttgctgtt ggagcatggg ggttcagggg gtgcagtatc
     1861 tgacgtcaat gccgagcgaa agcgagccga agggtagcat ttacgttaga taaccccctg
     1921 atatgctccg acgctttata tagaaaagaa gattcaacta ggtaaaatct taatataggt
     1981 tgagatgata aggtttataa ggaatttgtt tgttctaatt tttcactcat tttgttctaa
     2041 tttcttttaa caaatgttct ttttttttta gaacagttat gatatagtta gaatagttta
     2101 aaataaggag tgagaaaaag atgaaagaaa gatatggaac agtctataaa ggctctcaga
     2161 ggctcataga cgaagaaagt ggagaagtca tagaggtaga caagttatac cgtaaacaaa
     2221 cgtctggtaa cttcgtaaag gcatatatag tgcaattaat aagtatgtta gatatgattg
     2281 gcggaaaaaa acttaaaatc gttaactata tcctagataa tgtccactta agtaacaata
     2341 caatgatagc tacaacaaga gaaatagcaa aagctacagg aacaagtcta caaacagtaa
     2401 taacaacact taaaa
//
