LOCUS       CP030487                2467 bp    DNA     circular BCT 10-OCT-2019
DEFINITION  Staphylococcus aureus strain ER03913.3 plasmid unnamed5, complete
            sequence.
ACCESSION   CP030487
VERSION     CP030487.1
DBLINK      BioProject: PRJNA470993
            BioSample: SAMN09484030
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2467)
  AUTHORS   Sullivan,M.J., Altman,D.R., Chacko,K., Cliferri,B., Webster,E.,
            Deikus,G., Lewis,M., Khan,Z., Beckford,C., Rendo,A., Samaroo,F.,
            Sebra,R., Karam-Howlin,R., Southwick,K., Adams,E., Ying,L.,
            Kornblum,J., Factor,S., Danesh Yazdi,M., Dingle,T., Hamula,C.,
            Bashir,A., Schadt,E., Kasarskis,A., Patel,G., Wallach,F., Gibbs,K.
            and van Bakel,H.
  TITLE     Whole genome sequencing to identify and define MRSA outbreaks
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2467)
  AUTHORS   Sullivan,M.J., Altman,D.R., Chacko,K., Cliferri,B., Webster,E.,
            Deikus,G., Lewis,M., Khan,Z., Beckford,C., Rendo,A., Samaroo,F.,
            Sebra,R., Karam-Howlin,R., Southwick,K., Adams,E., Ying,L.,
            Kornblum,J., Factor,S., Danesh Yazdi,M., Dingle,T., Hamula,C.,
            Bashir,A., Schadt,E., Kasarskis,A., Patel,G., Wallach,F., Gibbs,K.
            and van Bakel,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JUN-2018) Genetics and Genomic Sciences, Icahn School
            of Medicine, One Gustave L. Levy Place Box 1498, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 340.704095187x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/29/2018 19:07:28
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS+
            Annotation Software revision      :: 4.5
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,216
            CDS (total)                       :: 3,134
            Genes (coding)                    :: 3,039
            CDS (coding)                      :: 3,039
            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)              :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 45 of 95
            Pseudo Genes (incomplete)         :: 42 of 95
            Pseudo Genes (internal stop)      :: 29 of 95
            Pseudo Genes (multiple problems)  :: 20 of 95
            ##Genome-Annotation-Data-END##
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..2467
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="ER03913.3"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA:New York City"
                     /lat_lon="40.7903114 N 73.9528738 W"
                     /collection_date="2015"
                     /collected_by="Mount Sinai Hospital"
     gene            477..536
                     /locus_tag="DQV49_16070"
     CDS             477..536
                     /locus_tag="DQV49_16070"
                     /inference="COORDINATES: protein motif:HMM:PF08253.9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QFK48780.1"
                     /translation="MDIFSIFVISTVSYQPNKK"
                     /name="hypothetical protein"
     gene            597..1331
                     /locus_tag="DQV49_16075"
     CDS             597..1331
                     /locus_tag="DQV49_16075"
                     /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="QFK48779.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALLLMAEVDISILSMVPREYF
                     HPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGID
                     DLNNISFEQFLSLFNSYKLFNK"
                     /name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
     gene            1777..2251
                     /locus_tag="DQV49_16080"
                     /pseudo=""
     CDS             1777..2251
                     /locus_tag="DQV49_16080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /name="replication/maintenance protein RepL"
     ARG             598..1328
                     /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"
     ARG             598..1331
                     /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="99.18"
                     /coverage="100.0"
     Typing          1778..2261
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.182"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataccaacat tatactctca ttatactaat tgcttattcc aatttcctat tggttggaac
       61 caacaggcgt tagtgtgttg ttgagttggt actttcatgg gattaatccc atgaaacccc
      121 caaccaactc gccaaagctt tggctaacac acacgccatt ccaaccaata gttttctcgg
      181 cataaagcca tgctctgacg cttaagtgca ctaatgcctt taaaaaacat taaagtctaa
      241 cacactagac ttatttactt cgtaattaag tcgttaaacc gtgtgctcta cgaccaaaac
      301 tataaaacct ttaagaactt tcttttttct tgtaaaaaaa gaaactagat aaatctctca
      361 tatcttttat tcaataatcg catcagattg cagtataaat ttaacgatca ctcatcatgt
      421 tcatatttat cagagctcgt gctataatta tactaatttt ataaggagga aaaaatatgg
      481 acatttttag tatttttgta atcagcacag ttagttatca accaaacaaa aaataagtgg
      541 ttataatgaa tcgttaataa gcaaaattca ttataaccaa attaaagagg gttataatga
      601 acgagaaaaa tataaaacac agtcaaaact ttattacttc aaaacataat atagataaaa
      661 taatgacaaa tataagatta aatgaacatg ataatatctt tgaaatcggc tcaggaaaag
      721 gccattttac ccttgaatta gtacagaggt gtaatttcgt aactgccatt gaaatagacc
      781 ataaattatg caaaactaca gaaaataaac ttgttgatca cgataatttc caagttttaa
      841 acaaggatat attgcagttt aaatttccta aaaaccaatc ctataaaata tttggtaata
      901 taccttataa cataagtaca gatataatac gcaaaattgt ttttgatagt atagctgatg
      961 agatttattt aatcgtggaa tacgggtttg ctaaaagatt attaaataca aaacgctcat
     1021 tggcattact tttaatggca gaagttgata tttctatatt aagtatggtt ccaagagaat
     1081 attttcatcc taaacctaaa gtgaatagct cacttatcag attaaataga aaaaaatcaa
     1141 gaatatcaca caaagataaa cagaagtata attatttcgt tatgaaatgg gttaacaaag
     1201 aatacaagaa aatatttaca aaaaatcaat ttaacaattc cttaaaacat gcaggaattg
     1261 acgatttaaa caatattagc tttgaacaat tcttatctct tttcaatagc tataaattat
     1321 ttaataagta agttaaggga tgcataaact gcatccctta acttgttttt cgtgtaccta
     1381 ttttttgtga atcgattatg tcttttgcgc attcgcttct tttctatata aatatgagcg
     1441 aagcgaataa gcgtcggaaa agcagcaaaa agtttccttt ttgctgttgg agcatggggg
     1501 ttcaggggtg cagtatctga cgtcaatgcc gagcgaaagc gagccgaagg gtagcattta
     1561 cgttagataa ccccctgata tgctccgacg ctttatatag aaaagaagat tcaactaggt
     1621 aaaatcttaa tataggttga gatgataagg tttataagga atttgtttgt tctaattttt
     1681 cactcatttt gttctaattt cttttaacaa atgttctttt tttttagaac agttatgata
     1741 tagttagaat agtttaaaat aaggagtgag aaaaagatga aagaaagata tggaacagtc
     1801 tataaaggct ctcagaggct catagacgaa gaaagtggag aagtcataga ggtagacaag
     1861 ttataccgta aacaaacgtc tggtaacttc gtaaaggcat atatagtgca attaataagt
     1921 atgttagata tgattggcgg aaaaaaactt aaaatcgtta actatatcct agataatgtc
     1981 cacttaagta acaatacaat gatagctaca acaagagaaa tagcaaaagc tacaggaaca
     2041 agtctacaaa cagtaataac aacacttaaa atcttagaag aaggaaatat tataaaaaga
     2101 aaaactggag tattaatgtt aaaccctgaa ctactaatga gaggcgacga ccaaaaacaa
     2161 aaatacctct tactcgaatt tgggactttg agcaagaggc aaatgaaaaa aagaaaatgc
     2221 attatctgat tattattctt tcaaggacta gtataacata aaatcgtcta caaatagaca
     2281 aaaaacctgc acgcttaatg tagatcaaaa gcttaacgca aatgaaatag attgacctcc
     2341 caataacacc acgtagttat tgggaggtca atctatgaaa tgcgattaag ctttttctaa
     2401 ttcgcataag cgtgcaggtt taaagtacat aaaaatataa tgaaaaaagc atcattatac
     2461 taacgtt
//
