LOCUS       CP127624                4536 bp    DNA     circular BCT 19-JUN-2023
DEFINITION  Staphylococcus aureus strain C289 plasmid pC289_2, complete
            sequence.
ACCESSION   CP127624
VERSION     CP127624.1
DBLINK      BioProject: PRJNA914892
            BioSample: SAMN32360922
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4536)
  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  JOURNAL   Unpublished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 4536)
  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                     :: C289
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 81x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/11/2023 02:04:16
            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)                     :: 2,823
            CDSs (total)                      :: 2,741
            Genes (coding)                    :: 2,675
            CDSs (with protein)               :: 2,675
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 66
            CDSs (without protein)            :: 66
            Pseudo Genes (ambiguous residues) :: 0 of 66
            Pseudo Genes (frameshifted)       :: 37 of 66
            Pseudo Genes (incomplete)         :: 30 of 66
            Pseudo Genes (internal stop)      :: 24 of 66
            Pseudo Genes (multiple problems)  :: 24 of 66
            ##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..4536
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="C289"
                     /isolation_source="Patient Sinus Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pC289_2"
                     /geo_loc_name="Australia: Adelaide"
                     /lat_lon="34.9285 S 138.6007 E"
                     /collection_date="2014-11-17"
                     /collected_by="ENT Surgery Department at the Queen
                     Elizabeth Hospital, Adelaide, Australia 123"
     gene            complement(join(4212..4536,1..230))
                     /locus_tag="PCM17_14085"
     CDS             complement(join(4212..4536,1..230))
                     /locus_tag="PCM17_14085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002502825.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF334 domain-containing protein"
                     /protein_id="WJA32441.1"
                     /translation="MNVLENLESNHEKTTLNLSNDDKLYLTRLTERIKHSNEHKINIEM
                     DDKLGKLIQQKIDKNLDKKIPDFHSTQTMERFKQSLLSIEQKQERLDDSLKSVHKWATY
                     FKSALMLTLFAVLLISVVATFMGGLFNVLGFDHMYKGLEYQIKHSEGFVAFLWHLGYLI
                     PYLLLATLIWLLFALERKYRY"
                     /name="DUF334 domain-containing protein"
     gene            complement(172..1023)
                     /locus_tag="PCM17_14090"
     CDS             complement(172..1023)
                     /locus_tag="PCM17_14090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011117537.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WJA32442.1"
                     /translation="MATTKLGNTKSASRAINYAEKRAEEKSGLNCDIDYAKSSFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAVYTHADTNHVHNHI
                     VINSIDLETGKKYQSNKKQREFVKQKNDEVCREHGLSVPERNASMRYTQAEKGLIEKGK
                     SSWKDEIRDAIEQSQATNFEELERELNQLDITIDRVTNKTITYRHLKENKKVRGKNLGA
                     QFDKGALENEFAVANERREFEQQLSKHEPTETEHRFRDTETHFERPRKLRIKSREDDFE
                     LE"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1010..1219)
                     /locus_tag="PCM17_14095"
     CDS             complement(1010..1219)
                     /locus_tag="PCM17_14095"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WJA32443.1"
                     /translation="MEQNKLRRLLFGIWILTVISLMILILFFNFSFLKQWWFIIICFLF
                     CAFGGLLIDYFIPKQRKGDTNGNN"
                     /name="hypothetical protein"
     gene            complement(1201..1584)
                     /gene="mobC"
                     /locus_tag="PCM17_14100"
     CDS             complement(1201..1584)
                     /gene="mobC"
                     /locus_tag="PCM17_14100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002449121.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WJA32444.1"
                     /translation="MSEQNDFVNGDETVGRNRKPNRKEPKQISFRVSESEYLKLQQSAE
                     TLNMSVPAFVKKKAQGSRLVAPKFDKETRQSIAKDLSKLGANANQIAKYCNQHQHETPN
                     YEALERNISELRERLDEVWNKIN"
                     /name="mobC"
     gene            1972..2394
                     /locus_tag="PCM17_14105"
     CDS             1972..2394
                     /locus_tag="PCM17_14105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018113513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WJA32445.1"
                     /translation="MPSSFNKKAKTINVNLTQDEYNKIQKLAEIRHLNPTSYTKQVALG
                     NRIKPTVIEYPQEQTTIEDDESTNNLHEVNEQLKKDNEALKSDVEAFRVKANLLDELLT
                     HVNENAYIDFNGFRDDEELRYKLKTIKQNEGGVTFE"
                     /name="hypothetical protein"
     gene            complement(2396..3340)
                     /locus_tag="PCM17_14110"
     CDS             complement(2396..3340)
                     /locus_tag="PCM17_14110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002958488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]; GO_function:
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA];
                     GO_process: GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WJA32439.1"
                     /translation="MSRKEQEIHSNQSTSQEVTNYTSTGYSNSRLSGNFFTTPQPELSF
                     DAMTIVGNLSRDNAQKLSSFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRIDLAFDFEDDLSDYYAMTDKAVK
                     KTVFYGRDGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVTSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWTATEKLKDQAMIYMLIHEEGTWGKLERHAKYKYKQLIKEISP
                     IDLTDLMKLTLKANEKQLQKQIDFWLLDAKREV"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            3723..4046
                     /gene="qacC"
                     /locus_tag="PCM17_14115"
     ARG             3724..4043
                     /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             3724..4046
                     /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(2424..3216)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.462"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(176..1023)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.286"
                     /coverage="100.0"
                     /evalue="2.28e-175"
ORIGIN
        1 aatcgctcca ttgtttgcgt tgaatgaaaa tctggaattt ttttatcgag gtttttatcg
       61 attttttgtt gtatcaattt gcctaactta tcatccatct caatattgat tttatgctca
      121 tttgagtgtt ttatccgttc agttaatcta gtgagatata acttgtcgtc attactcaag
      181 ttcaaagtcg tcttctcgtg atttgattct aagttttcta ggacgttcaa aatgcgtttc
      241 tgtgtctcta aatctgtgct cggtttcggt tggctcgtgt tttgataact gttgttcgaa
      301 ttctctccgt tcatttgcga ccgcaaactc attttctaat gcccccttat cgaattgtgc
      361 acctaaattt ttacctctca cttttttgtt ttctttcaag tgtctgtaag tgattgtttt
      421 gtttgtgaca cgatcgattg tgatgtctaa ttggttcaac tctctctcaa gctcctcaaa
      481 gtttgtcgct tgtgattgtt caatcgcatc tctaatttcg tctttccaag agcttttacc
      541 tttttcaatt aagccttttt cggcttgagt atatcgcatt gatgcgttgc gttcaggtac
      601 agacaatcca tgttctctac atacttcatc atttttttgt tttacgaact ctctttgttt
      661 tttattgctt tgatattttt tcccagtttc taaatcaatt gaattaatca caatatgatt
      721 gtgtacatgg tttgtatctg cgtgcgtata gacggctact tgatgattag gtgcaatctt
      781 ttctgccaat tctaaaccca attgattaca ttgctctggc gttacttcgc caggcttaaa
      841 cgattgaatc actgtatgtg cttgaacacc attctctttg ccatataaag ctcgtgtttg
      901 cttaaacgat gattttgcat aatctatatc acaatttaag ccactttttt cttctgctcg
      961 cttttctgcg taattgattg ctcgacttgc cgatttggta ttacctaatt tagttgttgc
     1021 cattggtatc cccctttctt tgtttaggga taaaataatc aatcaaaaga ccaccaaaag
     1081 cacaaaataa gaaacagatg atgataaacc accattgctt taggaatgaa aaattaaaaa
     1141 ataaaatcaa aatcattaaa gatataacag ttaaaatcca aataccaaac agcaatcttc
     1201 ttaatttatt ttgttccata cctcatctaa cctttcacgt aattcgctga tattacgctc
     1261 taatgcttca tagttcggcg tttcatgttg atgttgatta cagtactttg cgatttgatt
     1321 tgcattagca cctaatttac tcaaatcttt agcaatcgat tgtcgcgttt ctttatcaaa
     1381 ttttggtgcg actaatcgac tgccttgtgc ctttttcttt acgaaagcag gcacactcat
     1441 atttaaagtt tccgcagatt gttgtaactt taaatattcg gattcgctca cacgaaaact
     1501 aatttgtttt ggctccttac ggttgggttt acggtttcgc ccaacagttt cgtcgccatt
     1561 cacaaaatcg ttttgttcgc tcattaaatc ccaccacgct ttcttcgaaa gtcattactt
     1621 aatataaatc tagcttacag ggtaagccag attttatcaa gtaattatgt ggtttggcaa
     1681 gcgtcgtatt ttatagccac ttcgtgctaa aaataccggc ttgttgggga tattccccaa
     1741 tccccttatg atttttttct gccgaaaaaa atagtaatta ctagtgagta attactaaaa
     1801 cctaaatgct caaaaaagtg agcattataa ttgagtaatt actcatcaat ataaatatat
     1861 ttaaattgag tatttactca taaataacta atgctatttt aatttgtaat tactcataat
     1921 tatatgttga aatttattga gtaattacta atacataaag gtggttattt tatgcctagt
     1981 tcatttaata aaaaagcaaa aactataaat gttaacttaa ctcaagatga gtacaacaaa
     2041 atacaaaagc tagcagaaat tcgtcatctc aacccaacta gctataccaa gcaggttgct
     2101 ctaggtaatc ggatcaagcc tacagtgatt gaatatcctc aagaacaaac aacaattgag
     2161 gatgatgaat ctacgaataa cttgcatgaa gtcaatgaac agctcaaaaa ggacaacgag
     2221 gcactcaaat cagacgttga ggcattcaga gtaaaagcca accttttaga tgaacttctc
     2281 actcacgtga atgagaatgc ctatattgat ttcaatggtt ttagagacga tgaagaactc
     2341 agatataaac ttaaaaccat aaagcaaaac gaaggaggcg tgacctttga ataggtcaca
     2401 cctccctttt tgcgtcaagc aaccaaaaat ctatttgttt ttgcaattgt ttttcgttcg
     2461 cttttaaagt caatttcatt aaatctgtta aatcaattgg agatatttct ttaattaatt
     2521 gcttatattt atatttagca tgcctttcaa gttttcccca tgtgccttct tcatgaatta
     2581 acatataaat cattgcttgg tcttttaatt tttctgttgc agtccaatct ggtttcaaga
     2641 tatgtaaatc attaaaacaa tcattccagt aatccaccat atctctttta agttcaattt
     2701 ctacacgcca taagtgttca gacgtaactt caacatctgc attgtcttta cgttcttgtt
     2761 ttttgttata aattctaata aatctatcac tatcacgaac gccaaaatat tttgtttctg
     2821 gtttcccgtc acgaccataa aatacagttt tcttaactgc tttatcagtc attgcatagt
     2881 aatcactcaa atcatcttca aaatcaaaag ctaaatctat tcttgtaaaa ccatcatctt
     2941 ccatgtagtc gatgatgttt tgttttaacc aaagcatttc ttcatgtgta agtttatttg
     3001 gattaaattc aacacgcata ttacgtctat cccaagtatc tgctttcact ttgtcatact
     3061 cgatataaac tttttcttga agtgctttag ctttaaattt cgtttgtagt atatcccaaa
     3121 gtcttatttg aggttcgatg ctcataaatg acgatagctt ttgagcgttg tcacgactga
     3181 gatttccaac tattgtcata gcatcaaagc ttaattctgg ttgaggggtg gtaaaaaaat
     3241 taccacttaa ccggctatta gagtatccgg ttgaggtgta atttgtaact tcttgtgatg
     3301 tgctttgatt tgaatgaatt tcttgctctt ttctactcat aaaaaatcga ctccttaatt
     3361 taatttaaga agtcgcccac ccgaatattt atcttgatgt atatctcaat atcgtttaat
     3421 atctagatat acaaaatata aaaaaacaac ttagtgtttt ttctctgggt aagtcgcaca
     3481 caaactttgg tcggtgggtg ggcgacttct ttttttattt tgttattaat ataacactat
     3541 caaaaggctt ggtctaatca gatcaagaca agaagaaact cgttttcaac tcgtttcaaa
     3601 aacctttcaa aaaccatcaa tccacaaaaa taccacgcga atgacactca aaatacaaga
     3661 ctacaattaa aaaatactta gaataaaatt aaataaaata cgaaaattaa aaggagttaa
     3721 aaatgcctta tatttattta ataatagcca taagtactga agttattgga agtgcatttc
     3781 ttaaatcttc agaaggcttt tcaaaattta taccatcctt aggaacaata atttcatttg
     3841 gaatttgttt ctatttttta agtaaaacaa tgcaacacct accactaaat ataacttatg
     3901 caacttgggc gggactaggt ttagtcttaa caaccgtagt ctcaataatt attttcaaag
     3961 aacaaataaa tctaataact atagtatcta tagttttaat catagtcggc gtagtttcgt
     4021 taaacatttt cggaacatcg cattaattgc tttattccaa ttgctttatt gacgttgagc
     4081 ctcggaaccc ttaacaatcc caaaacttgt cgaatggtcg gcttaatagc tcacgctatg
     4141 ccgacattcg tctgcaagtt tagttaaggg ttcttctcaa catcaataaa ttttctcggc
     4201 ataaatgcgt gttaatatct atatttgcgt tctaaagcaa atagaagcca tataagcgtc
     4261 gctaatagta aataaggtat caagtatcct aaatgccata aaaacgctac aaagccctct
     4321 gagtgcttta tttgatattc tagcccttta tacatgtggt caaatcctaa aacattaaat
     4381 aaaccaccca tgaatgtagc gacaacgcta atcaataaaa cggcaaatag tgtcaacatc
     4441 aacgctgact taaagtaagt cgcccatttg tgtacgcttt taaggctatc atctagtctt
     4501 tcttgtttct gctcaatact taacaaagat tgcttg
//
