LOCUS       NZ_CP084483             2457 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Staphylococcus lugdunensis strain RMLUG1 plasmid pRMLUG1_3, complete
            sequence.
ACCESSION   NZ_CP084483
VERSION     NZ_CP084483.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21459164
            Assembly: GCF_026427435.1
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  JOURNAL   Unpublished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                   :: 510.82x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:03:30
            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)                     :: 2,554
            CDSs (total)                      :: 2,471
            Genes (coding)                    :: 2,426
            CDSs (with protein)               :: 2,426
            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)         :: 31 of 45
            Pseudo Genes (internal stop)      :: 11 of 45
            Pseudo Genes (multiple problems)  :: 12 of 45
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084483.1.
            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..2457
                     /organism="Staphylococcus lugdunensis"
                     /mol_type="genomic DNA"
                     /strain="RMLUG1"
                     /isolation_source="BALF"
                     /host="Homo sapiens"
                     /db_xref="taxon:28035"
                     /plasmid="pRMLUG1_3"
                     /geo_loc_name="China:Fujian"
                     /collection_date="2019-08-05"
     gene            complement(36..770)
                     /gene="erm(C)"
                     /locus_tag="LFR23_RS12755"
                     /old_locus_tag="LFR23_12760"
     ARG             complement(40..770)
                     /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"
     gene            complement(815..874)
                     /gene="ermCL"
                     /locus_tag="LFR23_RS12760"
                     /old_locus_tag="LFR23_12765"
     CDS             complement(815..874)
                     /gene="ermCL"
                     /locus_tag="LFR23_RS12760"
                     /old_locus_tag="LFR23_12765"
                     /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            complement(1569..2045)
                     /locus_tag="LFR23_RS12765"
                     /old_locus_tag="LFR23_12770"
     CDS             complement(1569..2045)
                     /locus_tag="LFR23_RS12765"
                     /old_locus_tag="LFR23_12770"
                     /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_267263023.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENVLSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             complement(37..770)
                     /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          complement(1560..2045)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.387"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acaagttaag ggatgcataa actgcatccc ttaacttact tattaaataa tttatagcta
       61 ttgaaaagag ataagaattg ttcaaagcta atattgttta aatcgtcaat tcctgcatgt
      121 tttaaggaat tgttaaattg attttttgta aatattttct tgtattcttt gttaacccat
      181 ttcataacga aataattata cttctgttta tctttgtgtg atattcttga tttttttcta
      241 tttaatctga taagtgagct attcacttta ggtttaggat gaaaatattc tcttggaacc
      301 atacttaata tagaaatatc aacttctgcc attaaaaata atgccaatga gcgttttgta
      361 tttaataatc ttttagcaaa cccgtattcc acgattaaat aaatctcatc agctatacta
      421 tcaaaaacaa ttttgcgtat tatatccgta cttatgttat aaggtatatt accaaatatt
      481 ttataggatt ggtttttagg aaatttaaac tgcaatatat ccttgtttaa aacttggaaa
      541 ttatcgtgat caacaagttt attttctgta gttttgcata atttatggtc tatttcaatg
      601 gcagttacga aattacacct ctgtactaat tcaagggtaa aatgcccttt tcctgagccg
      661 atttcaaaga tattatcatg ttcatttaat cttatatttg tcattatttt atctatatta
      721 tgttttgaag taataaagtt ttgactgtgt tttatatttt tctcgttcat tataaccctc
      781 tttaatttgc ttattaacga ttcattataa ccacttattt tttgtttggt tgataatgaa
      841 ctgtgctgat tacaaaaata ctaaaaatgc ccatattttt tcctccttat aaaattagta
      901 taattatagc acgagctctg ataaatatga acatgatgag tgatcgttaa atttatactg
      961 caatctgatg cgattattga ataaaagata tgagagattt atctagtttc tttttttaca
     1021 agaaaaaaga aagttcttaa aggttttata cttttggtcg tagagcacac ggtttaacga
     1081 cttaattacg aagtaaataa gtctagtgtg ttagacttta atgttttttt aaggcattag
     1141 tgcatttaag cgtcagagca tggctttatg ccgagaaaac tattggttgg aatggcgtgt
     1201 gtgttagcca aagctttggc gagttggttg ggggtttcat gggattaatc ccatgaaagt
     1261 accaactcaa caacacacta acgcctgttg gttccaacca ataggaaatt ggaataagca
     1321 attagtataa tgagagtata atgttggtat aacgttagta taatgatgct ttttttcatt
     1381 atatttttta tgtactttaa acctgcacgc ttatgtgaat tagaaaaagc ttaatcgcat
     1441 ttcatagatt gacctcccaa taactacgtg gtgttattgg gaggtcaatc tatttcattt
     1501 gcgttaagct tttgatctac attaagcgtg caggtttttt gtctatttgt agacgatttt
     1561 atgttatact agtccttgaa agaataataa tcagataata cattttcttg tttttcattt
     1621 gcctcttgct caaagttccc aaattcgagt aagaggtatt tttgtttttg gtcgtcgcct
     1681 ctcattagta gttcagggtt taacattaat actccagttt ttctttttat aatatttcct
     1741 tcttctaaga ttttaagtgt tgttattact gtttgtagac ttgttcctgt agcttttgct
     1801 atttctcttg ttgtagctat cattgtattg ttacttaagt ggacattatc taggatatag
     1861 ttaacgattt taagtttttt tccgccaatc atatctaaca tacttattaa ttgcactata
     1921 tatgccttta cgaagttacc agacgtttgt ttacggtata acttgtctac ctctatgact
     1981 tctccacttt cttcgtctat gagcctctga gagcctttat agactgttcc atatctttct
     2041 ttcatctttt tctcactcct tattttaaac tattctaact atatcataac tgttctaaaa
     2101 aaaaaagaac atttgttaaa agaaattaga acaaaatgag tgaaaaatta gaacaaacaa
     2161 attccttata aaccttatca tctcaaccta tattaagatt ttacctagtt gaatcttctt
     2221 ttctatataa agcgtcggag catatcaggg ggttatctaa cgtaaatgct acccttcggc
     2281 tcgctttcgc tcggcattga cgtcagatac tgcaccccct gaacccccat gctccaacag
     2341 caaaaaggaa actttttgct gcttttccga cgcttattcg cttcgctcat atttatatag
     2401 aaaagaagtg aatgcgcaaa agacataatc gattcacaaa aaataggtac acgaaaa
//
