LOCUS       NZ_CP092054             3125 bp    DNA     circular CON 03-MAY-2024
DEFINITION  Staphylococcus aureus strain USA300 plasmid pAH5667_2, complete
            sequence.
ACCESSION   NZ_CP092054
VERSION     NZ_CP092054.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25144899
            Assembly: GCF_022226995.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3125)
  AUTHORS   Horswill,A.R.
  TITLE     Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus
            Healthy Skin Isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3125)
  AUTHORS   Horswill,A.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-FEB-2022) Center for Genes, Environment & Health,
            Department of Immunology & Genomic Medicine, National Jewish Health,
            1400 Jackson St, Denver, CO 80206, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022226995.1-RS_2024_05_03
            Annotation Date                   :: 05/03/2024 04:25:54
            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)                     :: 2,847
            CDSs (total)                      :: 2,765
            Genes (coding)                    :: 2,696
            CDSs (with protein)               :: 2,696
            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)              :: 69
            CDSs (without protein)            :: 69
            Pseudo Genes (ambiguous residues) :: 0 of 69
            Pseudo Genes (frameshifted)       :: 38 of 69
            Pseudo Genes (incomplete)         :: 33 of 69
            Pseudo Genes (internal stop)      :: 13 of 69
            Pseudo Genes (multiple problems)  :: 14 of 69
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092054.1.
            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..3125
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="USA300"
                     /isolation_source="skin"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pAH5667_2"
                     /geo_loc_name="USA: Colorado"
                     /lat_lon="39.74 N 104.99 W"
                     /collection_date="2021"
                     /collected_by="Alexander R. Horswill"
     gene            join(3034..3125,1..904)
                     /locus_tag="AH5667_RS14210"
                     /old_locus_tag="AH5667_002692"
     CDS             join(3034..3125,1..904)
                     /locus_tag="AH5667_RS14210"
                     /old_locus_tag="AH5667_002692"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199892.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EKVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANVKAI
                     KPNRKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINASDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     gene            1487..1675
                     /locus_tag="AH5667_RS14215"
                     /old_locus_tag="AH5667_002693"
     CDS             1487..1675
                     /locus_tag="AH5667_RS14215"
                     /old_locus_tag="AH5667_002693"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001039248.1"
                     /translation="MNKNTVLDEGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     gene            complement(2001..2582)
                     /locus_tag="AH5667_RS14220"
                     /old_locus_tag="AH5667_002694"
     CDS             complement(2001..2582)
                     /locus_tag="AH5667_RS14220"
                     /old_locus_tag="AH5667_002694"
                     /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="WP_000991705.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     Typing          975..1139
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          2..904
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.889"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaaagaaa atagataatg taagctatgc agatatacta gaaattttaa aaatcaaaaa
       61 ggcttttaat gtaaaacaat gtggtaatat tttagaattt aagccaactg atgaaggcta
      121 tttgaagtta cataagacat ggttttgtaa atcaaaatta tgtccggttt gtaattggag
      181 acgtgctatg aaaaatagtt atcaagctca aaaagtgatt gaaaaagtaa ttaaggaaaa
      241 gccaaaagca cgttggttgt ttttaacact ttcaacaaaa aatgcgatag atggagatac
      301 tttagaacaa agtttgaagc atctaactaa agcatttgat aggttgagta gatataaaaa
      361 ggttaaacaa aatcttgttg gatttatgcg ttcaacagaa gttaccgtta ataaaaatga
      421 cggtagttat aatcagcaca tgcatgtttt gttatgtgtt gaaaatgcat attttagaaa
      481 aaaagagaat tatataactc aagaagaatg ggttaattta tggcaaagag cattacaagt
      541 tgactatcga cctgttgcta atgttaaagc gatcaaaccg aatagaaaag gcgataaaga
      601 cattgaatcg gcaatcaaag agacctcaaa atattcggtt aaatcatctg attttttaac
      661 tgatgatgat gaaaaaaatc aagaaattgt aagtgattta gaaaaaggtt tgtatcgaaa
      721 acgtatgtta agttatggtg gattgcttaa acaaaaacat aaaattttaa acttagacga
      781 tgtcgaagat ggtaatttga ttaatgcaag tgatgaagat aaaacaacag acgaagaaga
      841 aaaagcacat tcaattaccg caatttggaa tttcgaaaag caaaattatt atttaagaca
      901 ttagtgttga ctaatgtctt ttttgttgat tttttataaa aaagtactgt cttatttttg
      961 tgacaaatgc tgtatgtagt gtcacaaaaa taagacaaac gcaatatatt gtgtcacaaa
     1021 aataagacag tacagctttg tatgatatca ctttaaaata ccttaaaacc cctggaattt
     1081 ctggctttgc cagacctatc atttttgaat gatagcaaat tctccttatg ctcttacgga
     1141 gtttttagag aaaaattaaa aattctcgat ttttgataaa aaacgccctg caggaattta
     1201 gaaaaacatg tggaagtttt aaaggatttt atgctaattt ttaatttgca tgtaaatggg
     1261 cagtgttaaa aaattagtca ctggttttgc tgaaattttt gtttgtgaaa ttaccatata
     1321 tttatttggc tcatatttgc gttttaagag cttgtatata tttttaagtt aaaaacctat
     1381 atgatacccc ctaaaccttt aaaatacccc cttaaaactc aaaataaagg tatttataat
     1441 ttgagtaagt cttgtgataa agttttttaa aaaaggagtg tttattttga ataaaaacac
     1501 agtgttagat gaaggttacg ttatagcaac tattttaaat gttttctttt tacttggatt
     1561 aatttttata tctcatttgg aaaatttata tatattaatt ccgtatgtta ttttgatggg
     1621 aataaatgct atttatttgg ttgttaaggt tatgaatttc aaaaagaata attagaatat
     1681 ttgaggggat tttgaaacga gtttcttctt gttttcacac tgttttttta ttcctattgg
     1741 tgttgttgct tactttttgt ttttctataa agatgatgct tttgacgaga tggaagaaaa
     1801 atatgattat catgaagata ataaaaaata gacgacgcat ttatgccgag aaaatttatt
     1861 gatgttgaga agaaccctta actaaacttg cagacgaatg tcggcatagc gtgagctatt
     1921 aagccgacca ttcgacaagt tttgggattg ttaagggttc cgaggctcaa cgtcaataaa
     1981 gcaattggaa taaatagtat ctaaagtaac ccgtatttaa gattacattg tacatccttc
     2041 gaaaccatag tagctgcgat tccagctagg tttcctttta tcccaatttt agctaatttt
     2101 tttgctacgc cctttaagtt tttggcttta acatcttcaa aaactgctgt gattatgttt
     2161 ccagttaaaa gttctccata tgagtttaaa acttcagaat agaaacagtc accgctattt
     2221 ttgtagttcc caccaactgc tctaggtgat attgaactag ttttcttttt attctctatg
     2281 tcgtttttta gtttttggaa tccttcagga acatatccat atcgagattt ggcattttct
     2341 agattaacat ctttagctgt tccgtcttta tctaaaataa taattttgcc atatatgtat
     2401 tttagttctt tttcaatttc tttttcgttt aaagtttcaa cgtttttatc tgcaatgtta
     2461 tttttgtttt gggcttgagc ttctttgaaa ttaaaatcca agaccattga aagtatggtt
     2521 aaaatactta aagatactac taaaatcttt cttagtgata tactgttttg aattgcattc
     2581 attgtaaatg cccccttgtt ttgttattta aatgaattca atataatatt aacatataaa
     2641 aacaaaggag tttaatatga ataagttttt ttactttttg attattttat tatctgtatt
     2701 tttaattttt aattttgtta attcgatttt atttgataat ccttttgact ttttagaaag
     2761 ttttatttat tcattggttt tcacattaat ttatttaggt ttagagggtc ataaaaagaa
     2821 gaaggaatag gttgtttttt gaaacgagtg tgaacgagtt tcttcttgtc ttgatactat
     2881 atagaaataa ctcgatttta tatatatagc tgtaactgtt gatattacag tgtttaaacg
     2941 tgtttttgtg cgtgaaagga aaatttgaca ataaaaaacc ccagttatat tattaaggtg
     3001 tcgaatctta aataatactg ggggtctttt tatatgcaat ataatactac tagaagtata
     3061 accgaaaatc aagataataa aacgttaaaa gatatgacga aaagtgggaa acaacgccca
     3121 tggag
//
