LOCUS       NZ_CP047825             2473 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Staphylococcus aureus strain UP_1278 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP047825
VERSION     NZ_CP047825.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11175630
            Assembly: GCF_009912195.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Dilthey,A., Meyer,S. and Kaasch,A.
  TITLE     Increasing the efficiency of long-read sequencing for hybrid
            assembly with k-mer-based multiplexing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Dilthey,A., Meyer,S. and Kaasch,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JAN-2020) Institute for Medical Microbiology and
            Hospital Hygene, University Hospital Duesseldorf, Moorenstrasse 5,
            Duesseldorf 40225, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler Hybrid Assembly v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 43x / 446x
            Sequencing Technology :: Illumina MiSeq / Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/17/2023 03:56:23
            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)                     :: 2,814
            CDSs (total)                      :: 2,732
            Genes (coding)                    :: 2,647
            CDSs (with protein)               :: 2,647
            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)              :: 85
            CDSs (without protein)            :: 85
            Pseudo Genes (ambiguous residues) :: 0 of 85
            Pseudo Genes (frameshifted)       :: 47 of 85
            Pseudo Genes (incomplete)         :: 39 of 85
            Pseudo Genes (internal stop)      :: 19 of 85
            Pseudo Genes (multiple problems)  :: 18 of 85
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047825.1.
            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..2473
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="UP_1278"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed3"
     gene            complement(join(1912..2473,1..173))
                     /gene="erm(C)"
                     /locus_tag="E3T02_RS14050"
                     /old_locus_tag="E3T02_14050"
     CDS             complement(join(1912..2473,1..173))
                     /gene="erm(C)"
                     /locus_tag="E3T02_RS14050"
                     /old_locus_tag="E3T02_14050"
                     /EC_number="2.1.1.184"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011282421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /protein_id="WP_001003263.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYF
                     HPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGID
                     DLNNISFEQFLSLFNSYKLFNK"
                     /name="erm(C)"
     gene            complement(234..293)
                     /gene="ermCL"
                     /locus_tag="E3T02_RS14055"
                     /old_locus_tag="E3T02_14055"
     CDS             complement(234..293)
                     /gene="ermCL"
                     /locus_tag="E3T02_RS14055"
                     /old_locus_tag="E3T02_14055"
                     /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"
     gene            complement(988..1464)
                     /locus_tag="E3T02_RS14060"
                     /old_locus_tag="E3T02_14060"
     CDS             complement(988..1464)
                     /locus_tag="E3T02_RS14060"
                     /old_locus_tag="E3T02_14060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /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"
     ARG             complement(1913..2472)
                     /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="99.46"
                     /coverage="76.23"
     ARG             complement(4..173)
                     /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="100.0"
                     /coverage="23.36"
     Typing          complement(979..1464)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcagtta cgaaattaca cctctgtact aattcaaggg taaaatgccc ttttcctgag
       61 ccgatttcaa agatattatc atgttcattt aatcttatat ttgtcattat tttatctata
      121 ttatgttttg aagtaataaa gttttgactg tgttttatat ttttctcgtt cattataacc
      181 ctctttaatt tggttataat gaattttgct tattaacgat tcattataac cacttatttt
      241 ttgtttggtt gataatgaac tgtgctgatt acaaaaatac taaaaatgcc catatttttt
      301 cctccttata aaattagtat aattatagca cgagctctga taaatatgaa catgatgagt
      361 gatcgttaaa tttatactgc aatctgatgc gattattgaa taaaagatat gagagattta
      421 tctagtttct ttttttacaa gaaaaaagaa agttcttaaa ggttttatac ttttggtcgt
      481 agagcacacg gtttaacgac ttaattacga agtaaataag tctagtgtgt tagactttaa
      541 tgttttttta aggcattagt gcatttaagc gtcagagcat ggctttatgc cgagaaaact
      601 attggttgga atggcgtgtg tgttagccaa agctttggcg agttggttgg gggtttcatg
      661 ggattaatcc catgaaagta ccaactcaac aacacactaa cgcctgttgg ttccaaccaa
      721 taggaaattg gaataagcaa ttagtataat gagagtataa tgttggtata acgttagtat
      781 aatgatgctt tttttcatta tattttttat gtactttaaa cctgcacgct tatgtgaatt
      841 agaaaaagct taatcgcatt tcatagattg acctcccaat aactacgtgg tgttattggg
      901 aggtcaatct atttcatttg cgttaagctt ttgatctaca ttaagcgtgc aggttttttg
      961 tctatttgta gacgatttta tgttatacta gtccttgaaa gaataataat cagataatgc
     1021 attttcttgt ttttcatttg cctcttgctc aaagttccca aattcgagta agaggtattt
     1081 ttgtttttgg tcgtcgcctc tcattagtag ttcagggttt aacattaata ctccagtttt
     1141 tctttttata atatttcctt cttctaagat tttaagtgtt gttattactg tttgtagact
     1201 tgttcctgta gcttttgcta tttctcttgt tgtagctatc attgtattgt tacttaagtg
     1261 gacattatct aggatatagt taacgatttt aagttttttt ccgccaatca tatctaacat
     1321 acttattaat tgcactatat atgcctttac gaagttacca gacgtttgtt tacggtataa
     1381 cttgtctacc tctatgactt ctccactttc ttcgtctatg agcctctgag agcctttata
     1441 gactgttcca tatctttctt tcatcttttt ctcactcctt attttaaact attctaacta
     1501 tatcataact gttctaaaaa aaaaagaaca tttgttaaaa gaaattagaa caaaatgagt
     1561 gaaaaattag aacaaacaaa ttccttataa accttatcat ctcaacctat attaagattt
     1621 tacctagttg aatcttcttt tctatataaa gcgtcggagc atatcagggg gttatctaac
     1681 gtaaatgcta cccttcggct cgctttcgct cggcattgac gtcagatact gcaccccctg
     1741 aacccccatg ctccaacagc aaaaaggaaa ctttttgctg cttttccgac gcttattcgc
     1801 ttcgctcata tttatataga aaagaagtga atgcgcaaaa gacataatcg attcacaaaa
     1861 aataggtaca cgaaaaacaa gttaagggat gcagtttatg catcccttaa cttacttatt
     1921 aaataattta tagctattga aaagagataa gaattgttca aagctaatat tgtttaaatc
     1981 gtcaattcct gcatgtttta aggaattgtt aaattgattt tttgtaaata ttttcttgta
     2041 ttctttgtta acccatttca taacgaaata attatacttc tgtttatctt tgtgtgatat
     2101 tcttgatttt tttctattta atctgataag tgagctattc actttaggtt taggatgaaa
     2161 atattctctt ggaaccatac ttaatataga aatatcaact tctgccatta aaaataatgc
     2221 caatgagcgt tttgtattta ataatctttt agcaaacccg tattccacga ttaaataaat
     2281 ctcatcagct atactatcaa aaacaatttt gcgtattata tccgtactta tgttataagg
     2341 tatattacca aatattttat aggattggtt tttaggaaat ttaaactgca atatatcctt
     2401 gtttaaaact tggaaattat cgtgatcaac aagtttattt tctgtagttt tgcataattt
     2461 atggtctatt tca
//
