LOCUS       NZ_CP084446             2457 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Staphylococcus lugdunensis strain RMLUG6 plasmid pRMLUG6_2, complete
            sequence.
ACCESSION   NZ_CP084446
VERSION     NZ_CP084446.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21459169
            Assembly: GCF_026427535.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus lugdunensis
  ORGANISM  Staphylococcus lugdunensis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2457)
  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  JOURNAL   Unpublished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 2457)
  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                   :: 673.78x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:02:54
            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)                     :: 2,537
            CDSs (total)                      :: 2,454
            Genes (coding)                    :: 2,409
            CDSs (with protein)               :: 2,409
            Genes (RNA)                       :: 83
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 45
            CDSs (without protein)            :: 45
            Pseudo Genes (ambiguous residues) :: 0 of 45
            Pseudo Genes (frameshifted)       :: 16 of 45
            Pseudo Genes (incomplete)         :: 29 of 45
            Pseudo Genes (internal stop)      :: 12 of 45
            Pseudo Genes (multiple problems)  :: 11 of 45
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084446.1.
            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..2457
                     /organism="Staphylococcus lugdunensis"
                     /mol_type="genomic DNA"
                     /strain="RMLUG6"
                     /isolation_source="postoperative incision"
                     /host="Homo sapiens"
                     /db_xref="taxon:28035"
                     /plasmid="pRMLUG6_2"
                     /geo_loc_name="China:Wuhan"
                     /collection_date="2021-03-11"
     gene            join(2157..2457,1..176)
                     /locus_tag="LE189_RS12675"
                     /old_locus_tag="LE189_12680"
     CDS             join(2157..2457,1..176)
                     /locus_tag="LE189_RS12675"
                     /old_locus_tag="LE189_12680"
                     /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            871..930
                     /gene="ermCL"
                     /locus_tag="LE189_RS12680"
                     /old_locus_tag="LE189_12685"
     CDS             871..930
                     /gene="ermCL"
                     /locus_tag="LE189_RS12680"
                     /old_locus_tag="LE189_12685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002497446.1"
                     /translation="MGIFSIFVISTVHYQPNKK"
                     /name="ermCL"
     gene            975..1709
                     /gene="erm(C)"
                     /locus_tag="LE189_RS12685"
                     /old_locus_tag="LE189_12690"
     ARG             976..1706
                     /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             976..1709
                     /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..186
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.936"
                     /coverage="100.0"
                     /evalue="3.72e-89"
ORIGIN
        1 aagaaggaaa tattataaaa agaaaaactg gagtattaat gttaaaccct gaactactaa
       61 tgagaggcga cgaccaaaaa caaaaatacc tcttactcga atttgggaac tttgagcaag
      121 aggcaaatga aaaacaagaa aatgcattat ctgattatta ttctttcaag gactagtata
      181 acataaaatc gtctacaaat agacaaaaaa cctgcacgct taatgtagat caaaagctta
      241 acgcaaatga aatagattga cctcccaata acaccacgta gttattggga ggtcaatcta
      301 tgaaatgcga ttaagctttt tctaattcac ataagcgtgc aggtttaaag tacataaaaa
      361 atataatgaa aaaaagcatc attatactaa cgttatacca acattatact ctcattatac
      421 taattgctta ttccaatttc ctattggttg gaaccaacag gcgttagtgt gttgttgagt
      481 tggtactttc atgggattaa tcccatgaaa cccccaacca actcgccaaa gctttggcta
      541 acacacacgc cattccaacc aatagttttc tcggcataaa gccatgctct gacgcttaaa
      601 tgcactaatg ccttaaaaaa acattaaagt ctaacacact agacttattt acttcgtaat
      661 taagtcgtta aaccgtgtgc tctacgacca aaagtataaa acctttaaga actttctttt
      721 ttcttgtaaa aaaagaaact agataaatct ctcatatctt ttattcaata atcgcatcag
      781 attgcagtat aaatttaacg atcactcatc atgttcatat ttatcagagc tcgtgctata
      841 attatactaa ttttataagg aggaaaaaat atgggcattt ttagtatttt tgtaatcagc
      901 acagttcatt atcaaccaaa caaaaaataa gtggttataa tgaatcgtta ataagcaaat
      961 taaagagggt tataatgaac gagaaaaata taaaacacag tcaaaacttt attacttcaa
     1021 aacataatat agataaaata atgacaaata taagattaaa tgaacatgat aatatctttg
     1081 aaatcggctc aggaaaaggg cattttaccc ttgaattagt acagaggtgt aatttcgtaa
     1141 ctgccattga aatagaccat aaattatgca aaactacaga aaataaactt gttgatcacg
     1201 ataatttcca agttttaaac aaggatatat tgcagtttaa atttcctaaa aaccaatcct
     1261 ataaaatatt tggtaatata ccttataaca taagtacgga tataatacgc aaaattgttt
     1321 ttgatagtat agctgatgag atttatttaa tcgtggaata cgggtttgct aaaagattat
     1381 taaatacaaa acgctcattg gcattatttt taatggcaga agttgatatt tctatattaa
     1441 gtatggttcc aagagaatat tttcatccta aacctaaagt gaatagctca cttatcagat
     1501 taaatagaaa aaaatcaaga atatcacaca aagataaaca gaagtataat tatttcgtta
     1561 tgaaatgggt taacaaagaa tacaagaaaa tatttacaaa aaatcaattt aacaattcct
     1621 taaaacatgc aggaattgac gatttaaaca atattagctt tgaacaattc ttatctcttt
     1681 tcaatagcta taaattattt aataagtaag ttaagggatg cagtttatgc atcccttaac
     1741 ttgtttttcg tgtacctatt ttttgtgaat cgattatgtc ttttgcgcat tcacttcttt
     1801 tctatataaa tatgagcgaa gcgaataagc gtcggaaaag cagcaaaaag tttccttttt
     1861 gctgttggag catgggggtt cagggggtgc agtatctgac gtcaatgccg agcgaaagcg
     1921 agccgaaggg tagcatttac gttagataac cccctgatat gctccgacgc tttatataga
     1981 aaagaagatt caactaggta aaatcttaat ataggttgag atgataaggt ttataaggaa
     2041 tttgtttgtt ctaatttttc actcattttg ttctaatttc ttttaacaaa tgttcttttt
     2101 tttttagaac agttatgata tagttagaat agtttaaaat aaggagtgag aaaaagatga
     2161 aagaaagata tggaacagtc tataaaggct ctcagaggct catagacgaa gaaagtggag
     2221 aagtcataga ggtagacaag ttataccgta aacaaacgtc tggtaacttc gtaaaggcat
     2281 atatagtgca attaataagt atgttagata tgattggcgg aaaaaaactt aaaatcgtta
     2341 actatatcct agataatgtc cacttaagta acaatacaat gatagctaca acaagagaaa
     2401 tagcaaaagc tacaggaaca agtctacaaa cagtaataac aacacttaaa atcttag
//
