LOCUS       CP141401                6236 bp    DNA     circular BCT 10-JAN-2024
DEFINITION  Staphylococcus aureus strain Sau131 plasmid unnamed1, complete
            sequence.
ACCESSION   CP141401
VERSION     CP141401.1
DBLINK      BioProject: PRJNA1046723
            BioSample: SAMN38508060
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6236)
  AUTHORS   Nyasinga,J., Munshi,Z., Kigen,C., Nyerere,A., Musila,L. and
            Revathi,G.
  TITLE     Displacement of hospital-acquired methicillin-resistant
            Staphylococcus aureus clones by heterogenous community strains in
            Kenya over a 13-year period
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6236)
  AUTHORS   Nyasinga,J., Munshi,Z., Kigen,C., Musila,L. and Rivathi,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-NOV-2023) Pathology, Aga Khan University, Nairobi, 3rd
            Parklands Avenue, Nairobi, Nairobi 00100, Kenya
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-MAR-2023
            Assembly Method                   :: FLYE v. 2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 32x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/06/2023 16:08:46
            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)                     :: 2,950
            CDSs (total)                      :: 2,871
            Genes (coding)                    :: 1,794
            CDSs (with protein)               :: 1,794
            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)              :: 1,077
            CDSs (without protein)            :: 1,077
            Pseudo Genes (ambiguous residues) :: 0 of 1,077
            Pseudo Genes (frameshifted)       :: 1,032 of 1,077
            Pseudo Genes (incomplete)         :: 58 of 1,077
            Pseudo Genes (internal stop)      :: 29 of 1,077
            Pseudo Genes (multiple problems)  :: 41 of 1,077
            ##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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..6236
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Sau131"
                     /isolation_source="clinical"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="Kenya: Nyamira"
                     /lat_lon="0.5669 S 34.9341 E"
                     /collection_date="2023"
                     /collected_by="Aga Khan University Hospital, Nairobi"
                     /note="genotype: MRSA"
     gene            complement(join(5815..6236,1..570))
                     /locus_tag="UM768_14600"
                     /pseudo=""
     CDS             complement(join(5815..6236,1..570))
                     /locus_tag="UM768_14600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /name="protein rep"
     gene            1021..1602
                     /locus_tag="UM768_14605"
     CDS             1021..1602
                     /locus_tag="UM768_14605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WRM82925.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     gene            complement(1928..2115)
                     /locus_tag="UM768_14610"
                     /pseudo=""
     CDS             complement(1928..2115)
                     /locus_tag="UM768_14610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(2696..3689)
                     /locus_tag="UM768_14615"
                     /pseudo=""
     CDS             complement(2696..3689)
                     /locus_tag="UM768_14615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /name="protein rep"
     gene            4140..4721
                     /locus_tag="UM768_14620"
     CDS             4140..4721
                     /locus_tag="UM768_14620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WRM82924.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     gene            complement(5055..5234)
                     /locus_tag="UM768_14625"
                     /pseudo=""
     CDS             complement(5055..5234)
                     /locus_tag="UM768_14625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(2463..2627)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          complement(5582..5746)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          complement(4..570)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.526"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2697..3689)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.699"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5816..6236)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.528"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctaaaatat gcattttcaa cacataacaa aacatgcatg tgctgattat aactaccgtc
       61 atttttatta acggtaactt ctgttgaacg cataaatcca acaagatttt gtttaacctt
      121 tttatatcta ctcaacctat caaatgcttt agttagatgc ttcaaacttt gttctaaagt
      181 atctccatct atcgcatttt ttgttgaaag tgttaaaaac aaccaacgtg cttttggctt
      241 ttccttaatt actttttcaa tcactttttg agcttgataa ctatttttca tagcacgtct
      301 ccaattacaa accggacata attttgattt acaaaaccat gtcttatgta acttcaaata
      361 gccttcatca gttggcttaa attctaaaat attaccacat tgttttacat taaaagcctt
      421 tttgattttt aaaatttcta gtatatctgc atagcttaca ttatctattt tcttttctct
      481 ccatgggcgt tgtttcccac ttttcgtcat atcttttaac gttttattat cttgattttc
      541 ggttatactt ctagtagtat tatattgcat ataaaaagac ccccagtatt atttaagatt
      601 cgacacctta ataatataac tggggttttt tattgtcaaa ttttcctttc acgcacaaaa
      661 acacgtttaa acactgtaat atcaacagtt acagctatat atataaaatc gagttatttc
      721 tatatagtat caagacaaga agaaactcgt tcacactcgt ttcaaaaaac aacctattcc
      781 ttcttctttt tatgaccctc taaacctaaa taaattaatg tgaaaaccaa tgaataaata
      841 aaactttcta aaaagtcaaa aggattatca aataaaatcg aattaacaaa attaaaaatt
      901 aaaaatacag ataataaaat aatcaaaaag taaaaaactt attcatatta aactcctttg
      961 tttttatatg ttaatattat attgaattca tttaaataac aaaacaaggg ggcatttaca
     1021 atgaatgcaa ttcaaaacag tatatcacta agaaagattt tagtagtatc tttaagtatt
     1081 ttaaccatac tttcaatggt cttggatttt aatttcaaag aagctcaagc ccaaaacaaa
     1141 aataacattg cagataaaaa cgttgaaact ttaaacgaaa aagaaattga aaaagaacta
     1201 aaatacatat atggcaaaat tattatttta gataaagacg gaacagctaa agatgttaat
     1261 ctagaaaatg ccaaatctcg atatggatat gttcctgaag gattccaaaa actaaaaaac
     1321 gacatagaga ataaaaagaa aactagttca atatcaccta gagcagttgg tgggaactac
     1381 aaaaatagcg gtgactgttt ctattctgaa gttttaaact catatggaga acttttaact
     1441 ggaaacataa tcacagcagt ttttgaagat gttaaagcca aaaacttaaa gggcgtagca
     1501 aaaaaattag ctaaaattgg gataaaagga aacctagctg gaatcgcagc tactatggtt
     1561 tcgaaggatg tacaatgtaa tcttaaatac gggttacttt agatactatt tattccaatt
     1621 gctttattga cgttgagcct cggaaccctt aacaatccca aaacttgtcg aatggtcggc
     1681 ttaatagctc acgctatgcc gacattcgtc tgcaagttta gttaagggtt cttctcaaca
     1741 tcaataaatt ttctcggcat aaatgcgtcg tctatttttt attatcttca tgataatcat
     1801 atttttcttc catctcgtca aaagcatcat ctttatagaa aaacaaaaag taagcaacaa
     1861 caccaatagg aataaaaaaa cagtgtgaaa acaagaagaa actcgtttca aaatcccctc
     1921 aaatattcta attattcttt ttgaaattca taaccttaac aaccaaataa atagcattta
     1981 ttcccatcaa aataacatac ggaattaata tatataaatt ttccaaatga gatataaaaa
     2041 ttaatccaag taaaagaaaa catttaaaat agttgctata acgtaacctt catctaacac
     2101 tgtgttttta ttcaaaataa acactccttt tttaaaaaac tttatcacaa gacttactca
     2161 aattataaat acctttattt tgagttttaa ggggtatttt aaaggtttag ggggtatcat
     2221 ataggttttt aacttaaaaa tatatacaag ctcttaaaac gcaaatatga gccaaataaa
     2281 tatatggtaa tttcacaaac aaaaatttca gcaaaaccag tgactaattt tttaacactg
     2341 cccatttaca tgcaaattaa aaattagcat aaaatccttt aaaacttcca catgtttttc
     2401 taaattcctg cagggcgttt tttatcaaaa atcgagaatt tttaattttt ctctaaaaac
     2461 tccgtaagag cataaggaga atttgctatc attcaaaaat gataggtctg gcaaagccag
     2521 aaattccagg ggttttaagg tattttaaag tgatatcata caaagctgta ctgtcttatt
     2581 tttgtgacac aatatattgc gtttgtctta tttttgtgac actacataca gcatttgtca
     2641 caaaaataag acagtacttt tttataaaaa tcaacaaaaa agacattagt caacactaat
     2701 gtcttaaata ataattttgc ttttcgaaat tccaaattgc ggtaattgaa tgtgcttttt
     2761 cttcttcgtc tgttgtttta tcttcatcac ttgcattaat caaattacca tcttcgacat
     2821 cgtctaagtt taaaatttta tgtttttgtt taagcaatcc accataactt aacatacgtt
     2881 ttcgatacaa acctttttct aaatcactta caatttcttg attttttcat catcatcagt
     2941 taaaaaatca gatgatttaa ccgaatattt tgaggtctct ttgattgccg attcaatgtc
     3001 tttatcgcct tttctattcg gtttgatcgc tttaacatta gcaacaggtc gatagtcaac
     3061 ttgtaatgct ctttgccata aattaaccca ttcttcttga gttatataat tctctttttt
     3121 ctaaaatatg cattttcaac acataacaaa acatgcatgt gctgattata actaccgtca
     3181 tttttattaa cggtaacttc tgttgaacgc ataaatccaa caagattttg tttaaccttt
     3241 ttatatctac tcaacctatc aaatgcttta gttagatgct tcaaactttg ttctaaagta
     3301 tctccatcta tcgcattttt tgttgaaagt gttaaaaaca accaacgtgc ttttggcttt
     3361 tccttaatta ctttttcaat cactttttga gcttgataac tatttttcat agcacgtctc
     3421 caattacaaa ccggacataa ttttgattta caaaaccatg tcttatgtaa cttcaaatag
     3481 ccttcatcag ttggcttaaa ttctaaaata ttaccacatt gttttacatt aaaagccttt
     3541 ttgattttta aaatttctag tatatctgca tagcttacat tatctatttt cttttctctc
     3601 catgggcgtt gtttcccact tttcgtcata tcttttaacg ttttattatc ttgattttcg
     3661 gttatacttc tagtagtatt atattgcata taaaaagacc cccagtatta tttaagattc
     3721 gacaccttaa taatataact ggggtttttt attgtcaaat tttcctttca cgcacaaaaa
     3781 cacgtttaaa cactgtaata tcaacagtta cagctatata tataaaatcg agttatttct
     3841 atatagtatc aagacaagaa gaaactcgtt cacactcgtt tcaaaaaaca acctattcct
     3901 tcttcttttt atgaccctct aaacctaaat aaattaatgt gaaaaccaat gaataaataa
     3961 aactttctaa aaagtcaaaa ggattatcaa ataaaatcga attaacaaaa ttaaaaatta
     4021 aaaatacaga taataaaata atcaaaaagt aaaaaactta ttcatattaa actcctttgt
     4081 ttttatatgt taatattata ttgaattcat ttaaataaca aaacaagggg gcatttacaa
     4141 tgaatgcaat tcaaaacagt atatcactaa gaaagatttt agtagtatct ttaagtattt
     4201 taaccatact ttcaatggtc ttggatttta atttcaaaga agctcaagcc caaaacaaaa
     4261 ataacattgc agataaaaac gttgaaactt taaacgaaaa agaaattgaa aaagaactaa
     4321 aatacatata tggcaaaatt attattttag ataaagacgg aacagctaaa gatgttaatc
     4381 tagaaaatgc caaatctcga tatggatatg ttcctgaagg attccaaaaa ctaaaaaacg
     4441 acatagagaa taaaaagaaa actagttcaa tatcacctag agcagttggt gggaactaca
     4501 aaaatagcgg tgactgtttc tattctgaag ttttaaactc atatggagaa cttttaactg
     4561 gaaacataat cacagcagtt tttgaagatg ttaaagccaa aaacttaaag ggcgtagcaa
     4621 aaaaattagc taaaattggg ataaaaggaa acctagctgg aatcgcagct actatggttt
     4681 cgaaggatgt acaatgtaat cttaaatacg ggttacttta gatactattt attccaattg
     4741 ctttattgac gttgagcctc ggaaccctta acaatcccaa aacttgtcga atggtcggct
     4801 taatagctca cgctatgccg acattcgtct gcaagtttag ttaagggttc ttctcaacat
     4861 caataaattt tctcggcata aatgcgtcgt ctatttttta ttatcttcat gataatcata
     4921 tttttcttcc atctcgtcaa aagcatcatc tttatagaaa aacaaaaagt aagcaacaac
     4981 accaatagga ataaaaaaac agtgtgaaaa caagaagaaa ctcgtttcaa aatcccctca
     5041 aatattctaa ttattctttt gaaattcata accttaacaa ccaaataaat agcatttatt
     5101 cccatcaaaa taacatacgg aattaatata tataaatttt ccaaatgaga tataaaaatt
     5161 aatccaagta aaaagaaaac atttaaaata gttgctataa cgtaaccttc atctaacact
     5221 gtgtttttat tcaaaataaa cactcctttt taaaaaactt tatcacaaga cttactcaaa
     5281 ttataaatac ctttattttg agttttaagg gagtatttta aaggtttagg gggtatcata
     5341 taggttttta acttaaaaat atatacaagc tcttaaaacg caaatatgag ccaaataaat
     5401 atatggtaat ttcacaaaca aaaatttcag caaaaccagt gactaatttt ttaacactgc
     5461 ccatttacat gcaaattaaa aattagcata aaatccttta aaacttccac atgtttttct
     5521 aaattcctgc agggcgtttt ttatcaaaaa tcgagaattt ttaatttttc tctaaaaact
     5581 ccgtaagagc ataaggagaa tttgctatca ttcaaaaatg ataggtctgg caaagccaga
     5641 aattccaggg gttttaaggt attttaaagt gatatcatac aaagctgtac tgtcttattt
     5701 ttgtgacaca atatattgcg tttgtcttat ttttgtgaca ctacatacag catttgtcac
     5761 aaaaataaga cagtactttt tataaaaaat caacaaaaaa gacattagtc aacactaatg
     5821 tcttaaataa taattttgct ttcgaaattc caaattgcgg taattgaatg tgctttttct
     5881 tcttcgtctg ttgttttatc ttcatcactt gcattaatca aattaccatc ttcgacatcg
     5941 tctaagttta aaattttatg tttttgttta agcaatccac cataacttaa catacgtttt
     6001 cgatacaaac ctttttctaa atcacttaca atttcttgat tttttcatca tcatcagtta
     6061 aaaaatcaga tgatttaacc gaatattttg aggtctcttt gattgccgat tcaatgtctt
     6121 tatcgccttt tctattcggt ttgatcgctt taacattagc aacaggtcga tagtcaactt
     6181 gtaatgctct ttgccataaa ttaacccatt cttcttgagt tatataattc tctttt
//
