LOCUS       CP141382                3167 bp    DNA     circular BCT 10-JAN-2024
DEFINITION  Staphylococcus aureus strain Sau147 plasmid unnamed1, complete
            sequence.
ACCESSION   CP141382
VERSION     CP141382.1
DBLINK      BioProject: PRJNA1046723
            BioSample: SAMN38508072
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3167)
  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  JOURNAL   Unpublished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 3167)
  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                   :: 21x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/06/2023 16:15:03
            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)                     :: 3,034
            CDSs (total)                      :: 2,951
            Genes (coding)                    :: 1,795
            CDSs (with protein)               :: 1,795
            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)              :: 1,156
            CDSs (without protein)            :: 1,156
            Pseudo Genes (ambiguous residues) :: 0 of 1,156
            Pseudo Genes (frameshifted)       :: 1,116 of 1,156
            Pseudo Genes (incomplete)         :: 57 of 1,156
            Pseudo Genes (internal stop)      :: 39 of 1,156
            Pseudo Genes (multiple problems)  :: 54 of 1,156
            ##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..3167
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Sau147"
                     /isolation_source="clinical"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="Kenya: Nairobi"
                     /lat_lon="1.2921 S 36.8219 E"
                     /collection_date="2017"
                     /collected_by="Aga Khan University Hospital, Nairobi"
                     /note="genotype: MRSA"
     gene            complement(229..810)
                     /locus_tag="UM534_15165"
     CDS             complement(229..810)
                     /locus_tag="UM534_15165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WRM61612.1"
                     /translation="MNAIQKSVSLRKVLVISLSFLTILSMVLNFNFKEAQAQNKNNIAD
                     KNIETLNEKEIEKELDYIYGKIIVLDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKNSSISPRAVGGNYKNSNDCFYSEVLNSYGELLTGNIIAAVFDDVKAKNIKSAAKKL
                     ARIGIKGNLAGIAATMVSKDVQCTLKYGWF"
                     /name="hypothetical protein"
     gene            1262..2254
                     /locus_tag="UM534_15170"
                     /pseudo=""
     CDS             1262..2254
                     /locus_tag="UM534_15170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /name="protein rep"
     Typing          2325..2489
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.398"
                     /coverage="100.0"
                     /evalue="1.13e-79"
     Typing          1263..2254
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.386"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttagtaaatc agtgcacaat taatgtttta tttaagggat agttacacgc ataatcaaac
       61 atgcatttat gccgagaaaa tttattgatg ttgagaagaa cccttaacta aacttgaaga
      121 cgaatgtcgg catagcgtga gctattaagc cgacgattcg acaagtttag ggattgttaa
      181 gggttccgag gctcaacgtc aataaagcaa ttggaataaa ttatatattt agaaccatcc
      241 gtatttcaga gtacattgta catcctttga aaccatagta gctgcaattc cagctaaatt
      301 tccttttatg ccaattctgg ctaatttttt tgctgcactc tttatgtttt tggcttttac
      361 atcatcaaaa actgctgcga ttatattacc ggttaaaagt tctccatatg agtttaaaac
      421 ttcagaatag aaacagtcat tactattttt gtagtttcca ccaactgctc taggtgatat
      481 tgagctattt ttctttttat tctctatgtc gttctttagt ttttggaaac cttcaggaac
      541 atatccatat ctagatttgg cattttctag attaacatct ttagcggttc cgtctttatc
      601 taaaacaata attttgccat atatgtagtc tagttctttt tcgatttctt tttcgtttaa
      661 agtttcaatg tttttatctg cgatgttgtt tttgttttgg gcttgagctt ctttaaaatt
      721 aaaattcaag accattgaaa gtatagttaa aaaacttaaa gatattacta aaacttttct
      781 tagtgataca cttttttgaa ttgcattcat tataaatgcc cccttgtttt gttatttaaa
      841 tgaatccaat ataatattaa catataaaaa caaaggagtt taatatgaat aagtttattt
      901 attttttaat tgttttattg tccgtatttt taatatttaa ttttgttaat tcgattttat
      961 ttaataatcc ttttgacttt ttagaaagct ttatttattc gttggttttc acattgattt
     1021 atttaggttt agagggctat aaagagaaaa agaaatagat tgtttttgaa acgagttgaa
     1081 aacgagtttc ttcttgtctt gatactatat agaaataact cgattttata tatatagctg
     1141 taactgttga tattacagcg tttaaacgtg tttttgtgcg tgaaaggaaa atttgacaat
     1201 aaaaaacccc agttatatta ttaaggtgtc gaatcttaaa taatactggg ggtcttttta
     1261 tatgcaatat aatactacta gaagtataac cgaaaatcaa gataataaaa cgttaaaaga
     1321 tatgacgaaa agtgggaaac aacgcccatg gagagaaaag aaaatagata atgtaagcta
     1381 tgcagatata cttgaaattt taaaaataaa aaaggcttat aacgtaaaac aatgtggtaa
     1441 cgtcttagaa ttcaagccga ccgatgaagg ttatttgaaa ttacataaga cgtggttttg
     1501 taaatcaaag ctatgtccag tttgtaattg gaggcgtgct atgaaaaata gttatcaagc
     1561 tcaaaaagtg attgaagaag taattaagga aaagccaaaa gcacgttggt tgtttttaac
     1621 actttcaacc aaaaatgcga tagatggaga tactttagaa caaagtttga agcatctaac
     1681 taaagcattt gataggttga gtagatataa aaaggttaaa caaaatcttg ttggatttat
     1741 gcgttcaaca gaagttaccg ttaataaaaa tgatggtagt tataatcagc atatgcacgt
     1801 tttgttatgt gttgaaaatg catattttag aaaaaagaga attatataac tcaagaagaa
     1861 tgggttaatt tatggcaaaa agcattacaa gttgattatc gacctgttgc aaatattaaa
     1921 gcaattaaac ctaatcaaaa aggcgataaa gatattgaat cggcaatcaa agagacatca
     1981 aaatattcgg ttaagtcatc tgatttttaa ctgacaatga cgaaaaaatc aagaaattgt
     2041 aagtgattta gaaaaaggtt tatatcgaaa acgtatgtta agttatggtg gattgcttaa
     2101 acaaaagcat aaaattttaa acttagacga tgctgaagat ggtaatttaa ttaatacaag
     2161 tgatgaagat aaaataacag atgaagaagc aaaagcacat tcaattacgg caatttggaa
     2221 ttttgaaaaa caaaattatt atttaagaca ttagtgatga ctgatgtctt ttttattgat
     2281 tttttgtaaa aaagtactgt cttatttttg tgacaaatgc tgtatgtagt gtcacaaaac
     2341 tgtgacaaac gcaatatatt gtgtcacaaa agtgtgacac tacagctttt tatgatatca
     2401 ctttaaaatt acttaaaacc cttggaatgt ctggctttgc cagacctatc atttttgaat
     2461 gatagcaaat tctccttatg ctcttacgga gttcttagag aaaaattaaa aattctcgat
     2521 ttttgataaa aagcgccctg caggaattta gaaaaacatg gggaagtttt aaaggatttt
     2581 atgctaattt ttaatttgca tgtaaatggg cagtgtccga aaaatcgaca ctgggtttga
     2641 tcgaattttt gattataaaa aatttttgat tataaaatca gaatatattt atttggctca
     2701 tatttgcgtt ttaagaaaca aataagataa tacaggtata aaactatata tttttaaagt
     2761 tcgttctaaa taccccctta aaatgcaaaa taagtatatt cgattattac acgtaaattt
     2821 tggttttagc tcgacgcatt tttaagtatg taaatgcgcc tcttggataa cgaaaaataa
     2881 aaaatcttaa ttaaacagag tttaactaag atagtcacga attttattag gtttaaaaat
     2941 tatgattact tcagatgttt agaattaagg tgttgattat agtgtgaatg aaagcaaggg
     3001 ataataatta gtaaatcagt gcacaattaa tgttttattt aagggatagt tacacgcata
     3061 atcaaacatg catttatgcc gagaaaattt attgatgttg agaagaaccc ttaactaaac
     3121 ttgaagacga atgtcggcat agcgtgagct attaagccga cgattcg
//
