LOCUS       NZ_CP117980             5925 bp    DNA     circular CON 26-MAR-2024
DEFINITION  Staphylococcus aureus strain B-41012 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP117980
VERSION     NZ_CP117980.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33246705
            Assembly: GCF_028743615.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 5925)
  AUTHORS   Damerum,A.
  TITLE     Staphylococcus aureus B-41012 hifiasm Zymo Research D6300
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5925)
  AUTHORS   Damerum,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-FEB-2023) Microbiomics, Zymo Research Corporation,
            17062 Murphy Ave, Irvine, CA 92614, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Hifiasm v. 0.16.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology             :: PacBio Sequel IIe
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028743615.1-RS_2024_03_26
            Annotation Date                   :: 03/26/2024 01:59:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,685
            CDSs (total)                      :: 2,604
            Genes (coding)                    :: 2,531
            CDSs (with protein)               :: 2,531
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 73
            CDSs (without protein)            :: 73
            Pseudo Genes (ambiguous residues) :: 0 of 73
            Pseudo Genes (frameshifted)       :: 37 of 73
            Pseudo Genes (incomplete)         :: 29 of 73
            Pseudo Genes (internal stop)      :: 17 of 73
            Pseudo Genes (multiple problems)  :: 10 of 73
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117980.1.
            Bacteria and source DNA available from Annabelle Damerum, Zymo
            Research, 17062 Murphy Ave, Irvine, CA, United States, 92614.
            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..5925
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="B-41012"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA"
                     /collection_date="2021-08-05"
     gene            153..1157
                     /locus_tag="PT798_RS13380"
     CDS             153..1157
                     /locus_tag="PT798_RS13380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078098897.1"
                     /translation="MHSYTTRCIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTRNAIDGDHLEQSLKHMSKAFNKLKMYTKVKKNLIGFLRST
                     EVTVNKNDGSYNQHMHVLLCVESAYFKKQGQYIKQSEWVDLWQKALQVDYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            complement(1769..2092)
                     /gene="qacG"
                     /locus_tag="PT798_RS13385"
     CDS             complement(1769..2092)
                     /gene="qacG"
                     /locus_tag="PT798_RS13385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011100750.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quaternary ammonium compound efflux SMR
                     transporter QacG"
                     /protein_id="WP_015740450.1"
                     /translation="MHYLYLFISIATEIIGTSFLKTSEGFTKLWPTLGTLLSFGICFYF
                     LSLTIKFLPLNITYATWAGLGLVLTTIISVIVFKENVNLISIISIGLIVIGVVLLNVFG
                     ESH"
                     /name="qacG"
     gene            2369..3373
                     /locus_tag="PT798_RS13390"
     CDS             2369..3373
                     /locus_tag="PT798_RS13390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078098897.1"
                     /translation="MHSYTTRCIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTRNAIDGDHLEQSLKHMSKAFNKLKMYTKVKKNLIGFLRST
                     EVTVNKNDGSYNQHMHVLLCVESAYFKKQGQYIKQSEWVDLWQKALQVDYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     ARG             complement(3989..4308)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacG"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1773..2092)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacG"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            4585..5589
                     /locus_tag="PT798_RS13400"
     CDS             4585..5589
                     /locus_tag="PT798_RS13400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078098897.1"
                     /translation="MHSYTTRCIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTRNAIDGDHLEQSLKHMSKAFNKLKMYTKVKKNLIGFLRST
                     EVTVNKNDGSYNQHMHVLLCVESAYFKKQGQYIKQSEWVDLWQKALQVDYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     Typing          154..1157
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.532"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2370..3373
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.532"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4586..5589
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.532"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atagaaataa ttcaaagata taaaaagtcg tttgaatttt gatattacag cgtttttagc
       61 tatttttaac gtggaaaata aaatttgaca taaaaaaact ccagtaataa gattaaattg
      121 tcgagataaa atcaaatact ggaggttttt atatgcattc ttatactact agatgtatag
      181 acgaaaatca agataacgaa acattaaaag atatgacgaa aagtgggaaa caacgcccat
      241 ggagagagaa gaaaattgat aatgtaagtt atgcagatat actagaaatc ttaaaaatta
      301 aaaaagcttt taatgtaaaa caatgtggta acgtcttaga gttcaagcca actgatgaag
      361 gttatttaaa attacataag acatggtttt gtaagtcaaa attatgtcca gtttgtaatt
      421 ggaggcgtgc tatgaaaaat agttatcaag ctcaaagagt gattgaagaa gtggtaaaag
      481 aaaagccgaa agcacgttgg ttatttctca cattatcaac acgaaatgca atagatggtg
      541 accatttaga acaaagttta aaacatatgt ctaaggcttt taataaatta aaaatgtata
      601 caaaagttaa aaagaattta attggatttt tacgttcaac cgaagtaacg gttaataaaa
      661 atgacggtag ttataatcaa catatgcatg ttttattatg tgttgaaagt gcgtatttta
      721 aaaagcaagg tcagtatata aaacaaagtg agtgggtcga tttatggcaa aaagcattgc
      781 aagttgatta tcgaccagtc gcaaatatca aagcgatcaa accgaatcaa aaaggcgata
      841 aagatattca agcagctatc aaagagactt caaaatactc ggttaagtca tctgattttt
      901 taactgatga tgatgaaaga aatcaagaaa tcgtgaatga tttggaaaaa ggtttatacc
      961 gaaaacgtat gttgagttat ggtggattgc ttaaacaaaa acataaaatt ttaaatttag
     1021 acgatgccga agatggcaat ttgattaata caagtgacga agataaaaca acagacgaag
     1081 aagaaaaagc acactcaatt acggcaattt ggaattttga aaaacaaaat tattacttaa
     1141 aagatttgaa acgttagctt aaaagctagc gtttttttat gcttttttgc ccctgcggga
     1201 actatatcgt tcaacctgta tggttgacca gtttttatgc caatttttaa atttgcatgt
     1261 aactgggcag tgtctaaaaa attagtcact ggttttgctc aaatttttgt ttgtggaatt
     1321 agaatatatt tatttggctc atatttgcgt tttaaaagct tgtgtaggtt tttaggtata
     1381 aaactatatg atttaccctt aaatctttaa aatgccccct tagaattcaa aataaaggta
     1441 tttaaaattt ggtatctttg aaaatttaaa aataaaaaat gctaagtgca acaataaaaa
     1501 agttgtactt agcaataaca caaataatag aaaagctaat taatttaatt tttgagtact
     1561 atatttttcc tactcaattt gcttaattat aacataatta aagcatgcat ttatgccgag
     1621 aaaatttatt gatgttgaga agaaccctta actaaacttg cagacgaatg tcggcatagc
     1681 gtgagctatt aagccgatca ttcgacaagt tttgggattg ttaagggttc cgaggctcaa
     1741 cgtcaataaa gcaattggaa taaaataatc aatggctttc tccaaataca tttaagagca
     1801 ctacacctat aacaattaag ccaatagaaa ttatactaat taaattaaca ttttctttaa
     1861 aaacgataac tgagattatt gttgttaata ctaatcctag acctgcccat gttgcataag
     1921 ttatatttaa gggcaaaaat tttattgtta aacttaaaaa ataaaagcaa attccaaacg
     1981 aaagtagtgt acctaatgtt ggccataact ttgtgaaacc ctctgatgtt tttaaaaaac
     2041 tagttccgat tatttctgtt gcaattgaga taaataaata taaataatgc attaagcttc
     2101 tcctttaatt tctatttgat agcttatatt ttaacttata ttaagtgaaa gaaaaatttt
     2161 taagatttgt attttaaaac gagttgaaaa cgagtttctt cttgtcttga tactatatag
     2221 aaataattca aagatataaa aagtcgtttg aattttgata ttacagcgtt tttagctatt
     2281 tttaacgtgg aaaataaaat ttgacataaa aaaactccag taataagatt aaattgtcga
     2341 gataaaatca aatactggag gtttttatat gcattcttat actactagat gtatagacga
     2401 aaatcaagat aacgaaacat taaaagatat gacgaaaagt gggaaacaac gcccatggag
     2461 agagaagaaa attgataatg taagttatgc agatatacta gaaatcttaa aaattaaaaa
     2521 agcttttaat gtaaaacaat gtggtaacgt cttagagttc aagccaactg atgaaggtta
     2581 tttaaaatta cataagacat ggttttgtaa gtcaaaatta tgtccagttt gtaattggag
     2641 gcgtgctatg aaaaatagtt atcaagctca aagagtgatt gaagaagtgg taaaagaaaa
     2701 gccgaaagca cgttggttat ttctcacatt atcaacacga aatgcaatag atggtgacca
     2761 tttagaacaa agtttaaaac atatgtctaa ggcttttaat aaattaaaaa tgtatacaaa
     2821 agttaaaaag aatttaattg gatttttacg ttcaaccgaa gtaacggtta ataaaaatga
     2881 cggtagttat aatcaacata tgcatgtttt attatgtgtt gaaagtgcgt attttaaaaa
     2941 gcaaggtcag tatataaaac aaagtgagtg ggtcgattta tggcaaaaag cattgcaagt
     3001 tgattatcga ccagtcgcaa atatcaaagc gatcaaaccg aatcaaaaag gcgataaaga
     3061 tattcaagca gctatcaaag agacttcaaa atactcggtt aagtcatctg attttttaac
     3121 tgatgatgat gaaagaaatc aagaaatcgt gaatgatttg gaaaaaggtt tataccgaaa
     3181 acgtatgttg agttatggtg gattgcttaa acaaaaacat aaaattttaa atttagacga
     3241 tgccgaagat ggcaatttga ttaatacaag tgacgaagat aaaacaacag acgaagaaga
     3301 aaaagcacac tcaattacgg caatttggaa ttttgaaaaa caaaattatt acttaaaaga
     3361 tttgaaacgt tagcttaaaa gctagcgttt ttttatgctt ttttgcccct gcgggaacta
     3421 tatcgttcaa cctgtatggt tgaccagttt ttatgccaat ttttaaattt gcatgtaact
     3481 gggcagtgtc taaaaaatta gtcactggtt ttgctcaaat ttttgtttgt ggaattagaa
     3541 tatatttatt tggctcatat ttgcgtttta aaagcttgtg taggttttta ggtataaaac
     3601 tatatgattt acccttaaat ctttaaaatg cccccttaga attcaaaata aaggtattta
     3661 aaatttggta tctttgaaaa tttaaaaata aaaaatgcta agtgcaacaa taaaaaagtt
     3721 gtacttagca ataacacaaa taatagaaaa gctaattaat ttaatttttg agtactatat
     3781 ttttcctact caatttgctt aattataaca taattaaagc atgcatttat gccgagaaaa
     3841 tttattgatg ttgagaagaa cccttaacta aacttgcaga cgaatgtcgg catagcgtga
     3901 gctattaagc cgatcattcg acaagttttg ggattgttaa gggttccgag gctcaacgtc
     3961 aataaagcaa ttggaataaa ataatcaatg gctttctcca aatacattta agagcactac
     4021 acctataaca attaagccaa tagaaattat actaattaaa ttaacatttt ctttaaaaac
     4081 gataactgag attattgttg ttaatactaa tcctagacct gcccatgttg cataagttat
     4141 atttaagggc aaaaatttta ttgttaaact taaaaaataa aagcaaattc caaacgaaag
     4201 tagtgtacct aatgttggcc ataactttgt gaaaccctct gatgttttta aaaaactagt
     4261 tccgattatt tctgttgcaa ttgagataaa taaatataaa taatgcatta agcttctcct
     4321 ttaatttcta tttgatagct tatattttaa cttatattaa gtgaaagaaa aatttttaag
     4381 atttgtattt taaaacgagt tgaaaacgag tttcttcttg tcttgatact atatagaaat
     4441 aattcaaaga tataaaaagt cgtttgaatt ttgatattac agcgttttta gctattttta
     4501 acgtggaaaa taaaatttga cataaaaaaa ctccagtaat aagattaaat tgtcgagata
     4561 aaatcaaata ctggaggttt ttatatgcat tcttatacta ctagatgtat agacgaaaat
     4621 caagataacg aaacattaaa agatatgacg aaaagtggga aacaacgccc atggagagag
     4681 aagaaaattg ataatgtaag ttatgcagat atactagaaa tcttaaaaat taaaaaagct
     4741 tttaatgtaa aacaatgtgg taacgtctta gagttcaagc caactgatga aggttattta
     4801 aaattacata agacatggtt ttgtaagtca aaattatgtc cagtttgtaa ttggaggcgt
     4861 gctatgaaaa atagttatca agctcaaaga gtgattgaag aagtggtaaa agaaaagccg
     4921 aaagcacgtt ggttatttct cacattatca acacgaaatg caatagatgg tgaccattta
     4981 gaacaaagtt taaaacatat gtctaaggct tttaataaat taaaaatgta tacaaaagtt
     5041 aaaaagaatt taattggatt tttacgttca accgaagtaa cggttaataa aaatgacggt
     5101 agttataatc aacatatgca tgttttatta tgtgttgaaa gtgcgtattt taaaaagcaa
     5161 ggtcagtata taaaacaaag tgagtgggtc gatttatggc aaaaagcatt gcaagttgat
     5221 tatcgaccag tcgcaaatat caaagcgatc aaaccgaatc aaaaaggcga taaagatatt
     5281 caagcagcta tcaaagagac ttcaaaatac tcggttaagt catctgattt tttaactgat
     5341 gatgatgaaa gaaatcaaga aatcgtgaat gatttggaaa aaggtttata ccgaaaacgt
     5401 atgttgagtt atggtggatt gcttaaacaa aaacataaaa ttttaaattt agacgatgcc
     5461 gaagatggca atttgattaa tacaagtgac gaagataaaa caacagacga agaagaaaaa
     5521 gcacactcaa ttacggcaat ttggaatttt gaaaaacaaa attattactt aaaagatttg
     5581 aaacgttagc ttaaaagcta gcgttttttt atgctttttt gcccctgcgg gaactatatc
     5641 gttcaacctg tatggttgac cagtttttat gccaattttt aaatttgcat gtaactgggc
     5701 agtgtctaaa aaattagtca ctggttttgc tcaaattttt gtttgtggaa ttagaatata
     5761 tttatttggc tcatatttgc gttttaaaag cttgtgtagg tttttaggta taaaactata
     5821 tgatttaccc ttaaatcttt aaaatgcccc cttagaattc aaaataaagg tatttaaaat
     5881 ttggtatctt tgaaaattta aaaataaaaa atgctaagtg caaca
//
