LOCUS       NZ_CP115888             2473 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Staphylococcus aureus strain C308 plasmid pC308_1, complete
            sequence.
ACCESSION   NZ_CP115888
VERSION     NZ_CP115888.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32538168
            Assembly: GCF_027920385.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Bouras,G.
  TITLE     Hybrid Oxford Nanopore Technologies Illumina Sequences of 174
            Staphylococcus Aureus Isolates from Chronic Rhinosinusitis Patients
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Bouras,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-JAN-2023) Department of ENT Surgery at the Basil
            Hetzel Institute, Adelaide Medical School, The University of
            Adelaide, 37 Woodville Road, Woodville South, SA 5011, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 14-NOV-2022
            Assembly Method :: Flye for Genome, plassembler (Unicycler) for
            plasmids v. 2.9.1 (Flye) with short read polishing, 0.1.1
            (plassembler) with 0.5.0 (Unicycler)
            Assembly Name                     :: C308
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 01:06:43
            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)                     :: 2,825
            CDSs (total)                      :: 2,746
            Genes (coding)                    :: 2,657
            CDSs (with protein)               :: 2,657
            Genes (RNA)                       :: 79
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 89
            CDSs (without protein)            :: 89
            Pseudo Genes (ambiguous residues) :: 0 of 89
            Pseudo Genes (frameshifted)       :: 36 of 89
            Pseudo Genes (incomplete)         :: 48 of 89
            Pseudo Genes (internal stop)      :: 27 of 89
            Pseudo Genes (multiple problems)  :: 20 of 89
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP115888.1.
            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..2473
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="C308"
                     /isolation_source="Patient Sinus Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pC308_1"
                     /geo_loc_name="Australia: Adelaide"
                     /lat_lon="34.9285 S 138.6007 E"
                     /collection_date="2015-02-20"
                     /collected_by="ENT Surgery Department at the Queen
                     Elizabeth Hospital, Adelaide, Australia 1"
     gene            395..871
                     /locus_tag="PCM89_RS14100"
                     /old_locus_tag="PCM89_14100"
     CDS             395..871
                     /locus_tag="PCM89_RS14100"
                     /old_locus_tag="PCM89_14100"
                     /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            1566..1625
                     /gene="ermCL"
                     /locus_tag="PCM89_RS14105"
                     /old_locus_tag="PCM89_14105"
     CDS             1566..1625
                     /gene="ermCL"
                     /locus_tag="PCM89_RS14105"
                     /old_locus_tag="PCM89_14105"
                     /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            1686..2420
                     /gene="erm(C)"
                     /locus_tag="PCM89_RS14110"
                     /old_locus_tag="PCM89_14110"
     ARG             1687..2417
                     /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             1687..2420
                     /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          396..881
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtgaatcg attatgtctt ttgcgcattc acttcttttc tatataaata tgagcgaagc
       61 gaataagcgt cggaaaagca gcaaaaagtt tcctttttgc tgttggagca tgggggttca
      121 gggggtgcag tatctgacgt caatgccgag cgaaagcgag ccgaagggta gcatttacgt
      181 tagataaccc cctgatatgc tccgacgctt tatatagaaa agaagattca actaggtaaa
      241 atcttaatat aggttgagat gataaggttt ataaggaatt tgtttgttct aatttttcac
      301 tcattttgtt ctaatttctt ttaacaaatg ttcttttttt tttagaacag ttatgatata
      361 gttagaatag tttaaaataa ggagtgagaa aaagatgaaa gaaagatatg gaacagtcta
      421 taaaggctct cagaggctca tagacgaaga aagtggagaa gtcatagagg tagacaagtt
      481 ataccgtaaa caaacgtctg gtaacttcgt aaaggcatat atagtgcaat taataagtat
      541 gttagatatg attggcggaa aaaaacttaa aatcgttaac tatatcctag ataatgtcca
      601 cttaagtaac aatacaatga tagctacaac aagagaaata gcaaaagcta caggaacaag
      661 tctacaaaca gtaataacaa cacttaaaat cttagaagaa ggaaatatta taaaaagaaa
      721 aactggagta ttaatgttaa accctgaact actaatgaga ggcgacgacc aaaaacaaaa
      781 atacctctta ctcgaatttg ggaactttga gcaagaggca aatgaaaaac aagaaaatgc
      841 attatctgat tattattctt tcaaggacta gtataacata aaatcgtcta caaatagaca
      901 aaaaacctgc acgcttaatg tagatcaaaa gcttaacgca aatgaaatag attgacctcc
      961 caataacacc acgtagttat tgggaggtca atctatgaaa tgcgattaag ctttttctaa
     1021 ttcacataag cgtgcaggtt taaagtacat aaaaaatata atgaaaaaaa gcatcattat
     1081 actaacgtta taccaacatt atactctcat tatactaatt gcttattcca atttcctatt
     1141 ggttggaacc aacaggcgtt agtgtgttgt tgagttggta ctttcatggg attaatccca
     1201 tgaaaccccc aaccaactcg ccaaagcttt ggctaacaca cacgccattc caaccaatag
     1261 ttttctcggc ataaagccat gctctgacgc ttaaatgcac taatgcctta aaaaaacatt
     1321 aaagtctaac acactagact tatttacttc gtaattaagt cgttaaaccg tgtgctctac
     1381 gaccaaaagt ataaaacctt taagaacttt cttttttctt gtaaaaaaag aaactagata
     1441 aatctctcat atcttttatt caataatcgc atcagattgc agtataaatt taacgatcac
     1501 tcatcatgtt catatttatc agagctcgtg ctataattat actaatttta taaggaggaa
     1561 aaaatatggg catttttagt atttttgtaa tcagcacagt tcattatcaa ccaaacaaaa
     1621 aataagtggt tataatgaat cgttaataag caaaattcat tataaccaaa ttaaagaggg
     1681 ttataatgaa cgagaaaaat ataaaacaca gtcaaaactt tattacttca aaacataata
     1741 tagataaaat aatgacaaat ataagattaa atgaacatga taatatcttt gaaatcggct
     1801 caggaaaagg gcattttacc cttgaattag tacagaggtg taatttcgta actgccattg
     1861 aaatagacca taaattatgc aaaactacag aaaataaact tgttgatcac gataatttcc
     1921 aagttttaaa caaggatata ttgcagttta aatttcctaa aaaccaatcc tataaaatat
     1981 ttggtaatat accttataac ataagtacgg atataatacg caaaattgtt tttgatagta
     2041 tagctgatga gatttattta atcgtggaat acgggtttgc taaaagatta ttaaatacaa
     2101 aacgctcatt ggcattattt ttaatggcag aagttgatat ttctatatta agtatggttc
     2161 caagagaata ttttcatcct aaacctaaag tgaatagctc acttatcaga ttaaatagaa
     2221 aaaaatcaag aatatcacac aaagataaac agaagtataa ttatttcgtt atgaaatggg
     2281 ttaacaaaga atacaagaaa atatttacaa aaaatcaatt taacaattcc ttaaaacatg
     2341 caggaattga cgatttaaac aatattagct ttgaacaatt cttatctctt ttcaatagct
     2401 ataaattatt taataagtaa gttaagggat gcataaactg catcccttaa cttgtttttc
     2461 gtgtacctat ttt
//
