LOCUS       NZ_CP039166             2250 bp    DNA     circular CON 04-JUL-2021
DEFINITION  Staphylococcus aureus strain R46 plasmid pR46-2, complete sequence.
ACCESSION   NZ_CP039166
VERSION     NZ_CP039166.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11096691
            Assembly: GCF_005705635.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2250)
  AUTHORS   Ullah,N. and Ali,A.
  TITLE     Whole-genome sequencing of local methicillin-resistant S. aureus
            strain R46
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2250)
  AUTHORS   Ullah,N. and Ali,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-2019) Atta-ur-Rahman School of Applied
            Biosciences, National University of Sciences and Technology, H-12,
            Islamabad, Federal 44000, Pakistan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 08-DEC-2018
            Assembly Method                   :: SPAdes v. 3.9
            Assembly Name                     :: R46
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 30.0x
            Sequencing Technology             :: Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/04/2021 07:21:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,872
            CDSs (total)                      :: 2,802
            Genes (coding)                    :: 2,698
            CDSs (with protein)               :: 2,698
            Genes (RNA)                       :: 70
            rRNAs                             :: 6, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 33 of 104
            Pseudo Genes (incomplete)         :: 74 of 104
            Pseudo Genes (internal stop)      :: 15 of 104
            Pseudo Genes (multiple problems)  :: 17 of 104
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039166.1.
            Bacteria and source DNA available from Dr. Amjad Ali, ASAB,
            National University of Sciences and Technology, H-12, Islamabad,
            Pakistan.
            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..2250
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="R46"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pR46-2"
                     /geo_loc_name="Pakistan: Rawalpindi"
                     /lat_lon="33.5651 N 73.0169 E"
                     /collection_date="2017-10-03"
                     /collected_by="ASAB, National University of Sciences and
                     Technology, Islamabad"
     gene            complement(36..1019)
                     /locus_tag="E1951_RS14815"
                     /old_locus_tag="E1951_15135"
                     /pseudo=""
     CDS             complement(36..1019)
                     /locus_tag="E1951_RS14815"
                     /old_locus_tag="E1951_15135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000336291.1"
                     /note="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"
     gene            complement(1065..1265)
                     /locus_tag="E1951_RS14820"
                     /old_locus_tag="E1951_15140"
     CDS             complement(1065..1265)
                     /locus_tag="E1951_RS14820"
                     /old_locus_tag="E1951_15140"
                     /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="WP_138076850.1"
                     /translation="MAHKAPEKVSFFDGFELVLSYLDTYRNNVIFILVAERCVEVLVCM
                     CFKVLKTLKIGCTEKPHLLKL"
                     /name="hypothetical protein"
     gene            complement(1347..2117)
                     /gene="aadD1"
                     /locus_tag="E1951_RS14825"
                     /old_locus_tag="E1951_15145"
     ARG             complement(1351..2117)
                     /name="aadD1"
                     /gene="aadD1"
                     /gene_name="aminoglycoside O-nucleotidyltransferase
                     ANT(4')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1348..2117)
                     /name="ANT(4')-Ia"
                     /gene="ANT(4')-Ia"
                     /gene_name="ANT(4')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="101.19"
     Typing          complement(37..1040)
                     /name="rep_cluster_1018"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catctaatct tcaacaaact ggcccgtttg ttgaactact ctttaataaa ataatttttc
       61 cgttcccaat tccacattgc aataatagaa aatccatctt catcggcttt ttcgtcatca
      121 tctgtatgaa tcaaatcgcc ttcttctgtg tcatcaaggt ttaatttttt atgtatttct
      181 tttaacaaac caccatagga gattaacctt ttacggtgta aaccttcctc caaatcagac
      241 aaacgttaca aattcttttc ttcatcatcg gtcataaaat ccgtatcctt tacaggatat
      301 tttgcagttt cgtcaattgc cgattgtata tccgatttat atttattttt cggtcgaatc
      361 atttgaactt ttacatttgg atcatagtct aatttcattg cctttttcca aaattgaatc
      421 cattgttttt gattcacgta gttttctgta ttcttaaaat aagttggttc cacacatacc
      481 aatacatgca tgtgctgatt ataagaatta tctttattat ttattgtcac ttccgttgca
      541 cgcataaaac caacaagatt tttattaatt tttttatatt gcatcattcg gcgaaatcct
      601 tgagccatat ctgacaaact cttatttaat tcttcgccat cataaacatt tttaactgtt
      661 aatgtgagaa acaaccaacg aactgttggc ttttgtttaa taacttcagc aacaaccttt
      721 tgtgactgaa tgccatgttt cattgctctc ctccagttgc acattggaca aagcctggat
      781 ttacaaaacc acactcgata caactttctt tcgcctgttt cacgattttg tttatactct
      841 aatatttcag cacaatcttt tactctttca gcctttttaa attcaagaat atgcagaagt
      901 tcaaagtaat caacattagc gattttcttt tctctccatg gtctcacttt tccacttttt
      961 gtcttgtcca ctaaaaccct tgatttttca tctgaataaa tgctactatt aggacacata
     1021 atattaaaag aaacccccat ctatttagtt atttgtttag tcacttataa ctttaacaga
     1081 tggggttttt ctgtgcaacc aattttaagg gttttcaata ctttaaaaca catacatacc
     1141 aacacttcaa cgcacctttc agcaactaaa ataaaaatga cgttatttct atatgtatca
     1201 agataagaaa gaacaagttc aaaaccatca aaaaaagaca ccttttcagg tgctttatgc
     1261 gccatgacag ccatgataat tactaatact aggagaagtt aataaatacg taaccaacat
     1321 gattaacaat tattagaggt catcgttcaa aatggtatgc gttttgacac atccactata
     1381 tatccgtgtc gttctgtcca ctcctgaatc ccattccaga aattctctag cgattccaga
     1441 agtttctcag agtcggaaag ttgaccagac attacgaact ggcacagatg gtcataacct
     1501 gaaggaagat ctgattgctt aactgcttca gttaagaccg aagcgctcgt cgtataacag
     1561 atgcgatgat gcagaccaat caacatggca cctgccattg ctacctgtac agtcaaggat
     1621 ggtagaaatg ttgtcggtcc ttgcacacga atattacgcc atttgcctgc atattcaaac
     1681 agctcttcta cgataagggc acaaatcgca tcgtggaacg tttgggcttc taccgattta
     1741 gcagtttgat acactttctc taagtatcca cctgaatcat aaatcggcaa aatagagaaa
     1801 aattgaccat gtgtaagagg ccaatctgat tccacctgag atgcataatc tagtagaatc
     1861 tcttcgctat caaaattcac ttccaccttc cactcaccgg ttgtccattc atggctgaac
     1921 tctgcttcct ctgttgacat gacacacatc atctcaatat ccgaataggg cccatcagtc
     1981 tgacgaccaa gagagccata aacaccaata gccttaacat catccccata tttatccaat
     2041 attcgttcct taatttcatg aacaatcttc attctttctt ctctagtcat tattattggt
     2101 ccattcacta ttctcattcc cttttcagat aattttagat ttgcttttct aaataagaat
     2161 atttggagag caccgttctt attcagctat taataactcg tcttcctaag catccttcaa
     2221 tccttttaat aacaattata gcatctaatc
//
