LOCUS       NZ_CP038851             2474 bp    DNA     circular CON 04-JUL-2021
DEFINITION  Staphylococcus aureus strain Lr2 plasmid pLr2-1, complete sequence.
ACCESSION   NZ_CP038851
VERSION     NZ_CP038851.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11096030
            Assembly: GCF_005706855.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2474)
  AUTHORS   Ullah,N. and Ali,A.
  TITLE     Whole-genome sequencing of local methicillin-resistant S. aureus
            strain Lr2
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2474)
  AUTHORS   Ullah,N. and Ali,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-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                     :: 04-DEC-2018
            Assembly Method                   :: SPAdes v. 3.9
            Assembly Name                     :: Lr2
            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 07:29:43
            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)                     :: 2,863
            CDSs (total)                      :: 2,792
            Genes (coding)                    :: 2,669
            CDSs (with protein)               :: 2,669
            Genes (RNA)                       :: 71
            rRNAs                             :: 6, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 34 of 123
            Pseudo Genes (incomplete)         :: 84 of 123
            Pseudo Genes (internal stop)      :: 27 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038851.1.
            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..2474
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Lr2"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pLr2-1"
                     /geo_loc_name="Pakistan: Lahore"
                     /lat_lon="31.5204 N 74.3587 E"
                     /collection_date="2017-11-04"
                     /collected_by="ASAB, National University of Sciences and
                     Technology, Islamabad"
     gene            complement(27..503)
                     /locus_tag="E1948_RS14690"
                     /old_locus_tag="E1948_14930"
     CDS             complement(27..503)
                     /locus_tag="E1948_RS14690"
                     /old_locus_tag="E1948_14930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     gene            complement(952..1686)
                     /gene="erm(C)"
                     /locus_tag="E1948_RS14695"
                     /old_locus_tag="E1948_14935"
     ARG             complement(956..1686)
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1747..1806)
                     /gene="ermCL"
                     /locus_tag="E1948_RS14700"
                     /old_locus_tag="E1948_14940"
     CDS             complement(1747..1806)
                     /gene="ermCL"
                     /locus_tag="E1948_RS14700"
                     /old_locus_tag="E1948_14940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002497446.1"
                     /translation="MGIFSIFVISTVHYQPNKK"
                     /name="ermCL"
     ARG             complement(953..1686)
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          complement(18..503)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctatttgtag acgattttat gttatactag tccttgaaag aataataatc agataatgca
       61 ttttcttgtt tttcatttgc ctcttgctca aagttcccaa attcgagtaa gaggtatttt
      121 tgtttttggt cgtcgcctct cattagtagt tcagggttta acattaatac tccagttttt
      181 ctttttataa tatttccttc ttctaagatt ttaagtgttg ttattactgt ttgtagactt
      241 gttcctgtag cttttgctat ttctcttgtt gtagctatca ttgtattgtt acttaagtgg
      301 acattatcta ggatatagtt aacgatttta agtttttttc cgccaatcat atctaacata
      361 cttattaatt gcactatata tgcctttacg aagttaccag acgtttgttt acggtataac
      421 ttgtctacct ctatgacttc tccactttct tcgtctatga gcctctgaga gcctttatag
      481 actgttccat atctttcttt catctttttc tcactcctta ttttaaacta ttctaactat
      541 atcataactg ttctaaaaaa aaaaagaaca tttgttaaaa gaaattagaa caaaatgagt
      601 gaaaaattag aacaaacaaa ttccttataa accttatcat ctcaacctat attaagattt
      661 tacctagttg aatcttcttt tctatataaa gcgtcggagc atatcagggg gttatctaac
      721 gtaaatgcta cccttcggct cgctttcgct cggcattgac gtcagatact gcaccccctg
      781 aacccccatg ctccaacagc aaaaaggaaa ctttttgctg cttttccgac gcttattcgc
      841 ttcgctcata tttatataga aaagaagtga atgcgcaaaa gacataatcg attcacaaaa
      901 aataggtaca cgaaaaacaa gttaagggat gcataaactg catcccttaa cttacttatt
      961 aaataattta tagctattga aaagagataa gaattgttca aagctaatat tgtttaaatc
     1021 gtcaattcct gcatgtttta aggaattgtt aaattgattt tttgtaaata ttttcttgta
     1081 ttctttgtta acccatttca taacgaaata attatacttc tgtttatctt tgtgtgatat
     1141 tcttgatttt tttctattta atctgataag tgagctattc actttaggtt taggatgaaa
     1201 atattctctt ggaaccatac ttaatataga aatatcaact tctgccatta aaaataatgc
     1261 caatgagcgt tttgtattta ataatctttt agcaaacccg tattccacga ttaaataaat
     1321 ctcatcagct atactatcaa aaacaatttt gcgtattata tccgtactta tgttataagg
     1381 tatattacca aatattttat aggattggtt tttaggaaat ttaaactgca atatatcctt
     1441 gtttaaaact tggaaattat cgtgatcaac aagtttattt tctgtagttt tgcataattt
     1501 atggtctatt tcaatggcag ttacgaaatt acacctctgt actaattcaa gggtaaaatg
     1561 cccttttcct gagccgattt caaagatatt atcatgttca tttaatctta tatttgtcat
     1621 tattttatct atattatgtt ttgaagtaat aaagttttga ctgtgtttta tatttttctc
     1681 gttcattata accctcttta atttggttat aatgaatttt gcttattaac gattcattat
     1741 aaccacttat tttttgtttg gttgataatg aactgtgctg attacaaaaa tactaaaaat
     1801 gcccatattt tttcctcctt ataaaattag tataattata gcacgagctc tgataaatat
     1861 gaacatgatg agtgatcgtt aaatttatac tgcaatctga tgcgattatt gaataaaaga
     1921 tatgagagat ttatctagtt tcttttttta caagaaaaaa gaaagttctt aaaggtttta
     1981 tacttttggt cgtagagcac acggtttaac gacttaatta cgaagtaaat aagtctagtg
     2041 tgttagactt taatgttttt ttaaggcatt agtgcattta agcgtcagag catggcttta
     2101 tgccgagaaa actattggtt ggaatggcgt gtgtgttagc caaagctttg gcgagttggt
     2161 tgggggtttc atgggattaa tcccatgaaa gtaccaactc aacaacacac taacgcctgt
     2221 tggttccaac caataggaaa ttggaataag caattagtat aatgagagta taatgttggt
     2281 ataacgttag tataatgatg ctttttttca ttatattttt tatgtacttt aaacctgcac
     2341 gcttatgtga attagaaaaa gcttaatcgc atttcataga ttgacctccc aataactacg
     2401 tggtgttatt gggaggtcaa tctatttcat ttgcgttaag cttttgatct acattaagcg
     2461 tgcaggtttt ttgt
//
