LOCUS       CP127546                2241 bp    DNA     circular BCT 19-JUN-2023
DEFINITION  Staphylococcus aureus strain C878 plasmid pC878_2, complete
            sequence.
ACCESSION   CP127546
VERSION     CP127546.1
DBLINK      BioProject: PRJNA914892
            BioSample: SAMN32360962
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2241)
  AUTHORS   Bouras,G., Houtak,G., Nepal,R., Shaghayegh,G. and Vreugde,S.
  TITLE     Hybrid Oxford Nanopore Technologies Illumina Sequences of 174
            Staphylococcus Aureus Isolates from Chronic Rhinosinusitis Patients
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2241)
  AUTHORS   Bouras,G., Houtak,G., Nepal,R., Shaghayegh,G. and Vreugde,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-JUN-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                     :: C878
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 88x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/11/2023 01:57:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,779
            CDSs (total)                      :: 2,696
            Genes (coding)                    :: 2,631
            CDSs (with protein)               :: 2,631
            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)              :: 65
            CDSs (without protein)            :: 65
            Pseudo Genes (ambiguous residues) :: 0 of 65
            Pseudo Genes (frameshifted)       :: 39 of 65
            Pseudo Genes (incomplete)         :: 30 of 65
            Pseudo Genes (internal stop)      :: 21 of 65
            Pseudo Genes (multiple problems)  :: 24 of 65
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2241
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="C878"
                     /isolation_source="Patient Sinus Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pC878_2"
                     /geo_loc_name="Australia: Adelaide"
                     /lat_lon="34.9285 S 138.6007 E"
                     /collection_date="2020-03-09"
                     /collected_by="ENT Surgery Department at the Queen
                     Elizabeth Hospital, Adelaide, Australia 163"
     gene            complement(join(1828..2241,1..585))
                     /locus_tag="PCL44_13890"
     CDS             complement(join(1828..2241,1..585))
                     /locus_tag="PCL44_13890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001160226.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WIY92543.1"
                     /translation="MQYNTTKYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGEHLEQSLKYMSKAFNKLKMYAKVKKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            913..1236
                     /gene="qacC"
                     /locus_tag="PCL44_13895"
     ARG             914..1233
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             914..1236
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.96"
                     /coverage="100.0"
     Typing          complement(11..585)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.138"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1829..2241)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataattctct ttttttctga aataagcatt ttcaacacac aataaaacgt gcatatgttg
       61 attataactt ccgtcatttt tgttaactgt aacttcagtt gaacgcataa aaccgattaa
      121 attcttttta acttttgcat acatttttaa cttgttaaaa gctttcgaca tatattttaa
      181 actctgttct aaatgctcac catctatcgc attttttgtt gaaagtgtta agaataacca
      241 acgtgctttt ggcttttctt taaccactgc ttcaatgact ttttgagctt gataactatt
      301 tttcattgaa cgcctccaat tacaaaccgg acataattta gacttacaaa accatgtttt
      361 ataaagtttt aaataccctt catcagtcgg cttaaattct aagacgttac cacattgctt
      421 cacgttaaaa gcctttttaa tttttaaaat ttctagtata tctgcataac ttacattgtc
      481 gattttcttt tctctccatg ggcgttgtgt cccactttta gtcatatctt tcaatgtttc
      541 attatcttga ttttcgtcta tatattttgt agtattatat tgcatataaa aagacctcca
      601 gttttgattt agattcgaca ccttaatcat ataactgggg tttttttatg tcaatttttt
      661 ctttcacgct aaaaaaacaa cacaaatgtt gtcataccaa cgtttttaaa acattttaat
      721 tctttgagtt atttctatat agtatcaaga caagaagaaa ctcgttttca actcgtttca
      781 aaaacctttc aaaaaccatc aatccacaaa aataccacgc gaatgacact caaaatacaa
      841 gactacaatt aaaaaatact ttacaattaa aaaatactta gaataaaata cgaaaattaa
      901 aaggagctaa aaatgcctta tatttattta ataatagcca taagtactga agttattgga
      961 agtgcatttc ttaaatcttc agaaggcttt tcaaaattta taccatcctt aggaacaata
     1021 atttcatttg gaatttgttt ctatttttta agtaaaacaa tgcaacacct accactaaat
     1081 ataacttatg caacttgggc gggactaggt ttagtcttaa caaccgtagt ctcaataatt
     1141 attttcaaag aacaaataaa tctaataact atagtatcta tagttttaat catagtcggc
     1201 gtagtttcgt taaacatttt cggaacatcg cattaattgc tttattccaa ttgctttatt
     1261 gacgttgagc ctcggaaccc ttaacaatcc caaaacttgt cgaatggtcg gcttaatagc
     1321 tcacgctatg ccgacattcg tctccaagtt tagttaaggg ttcttctcaa catcaataaa
     1381 ttttctcggc ataaatgctg tgttataatt aaaattcctt tcttgatcta tttttcactg
     1441 ataacaccta aatattaaaa cagtgcatat aagagctacc aaaattttta agggtagctc
     1501 tttatttttt gttcaaacat ttattcaaaa tcagaatacc tttattttta attttaaggg
     1561 gtcattttaa agaattaagg gttatttata tagttttata cctaaaaacc taaatcggct
     1621 cttaaaacgc aaatgagagc caaataaaaa taattgcttt tcacaaacaa aaatttgagc
     1681 aaaaccagtg tcgaattttt tagacactgc ccatttacat gcaaatttaa aaattagcat
     1741 aaaaaatggg caaccatgcc ggttgaacgc tatagttcct gcaggggcaa aaaagcataa
     1801 aaaaacgcta gctttgataa gctaacgtta caaatttttt aagaaataat tttgtttttc
     1861 aaaattccaa atggccgtaa ttgaatgggc tttttgttct tcttcagtcg ttttttcttc
     1921 atcgctcgtt tgaattaaat taccttcttc ggcatcgtct aaatttaaaa gtttatgttt
     1981 ttgtttaagt aaaccaccgt aacttaacat acgttttctg tataaacctt gttctaaatc
     2041 ttgaacaatt tctgcgtctt tttcatggtt tcctgttaaa taatcggacg acttaaccga
     2101 gtattttgat gtctctttaa ttgcagcttg tatatcttta tcgccttttt tattcggctt
     2161 aattgctttg atatttgcga ctggtttgta atcaacttga agagcttttt gccataaatt
     2221 gatccactct tcttgcgtta t
//
