LOCUS       NZ_CP033816             2366 bp    DNA     circular CON 14-JUL-2023
DEFINITION  Streptococcus pyogenes strain FDAARGOS_514 plasmid unnamed, complete
            sequence.
ACCESSION   NZ_CP033816
VERSION     NZ_CP033816.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163208
            Assembly: GCF_003812725.1
KEYWORDS    RefSeq.
SOURCE      Streptococcus pyogenes
  ORGANISM  Streptococcus pyogenes
            Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae;
            Streptococcus.
REFERENCE   1  (bases 1 to 2366)
  AUTHORS   Goldberg,B., Campos,J., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2366)
  AUTHORS   Goldberg,B., Campos,J., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-NOV-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.4, SPAdes v. 3.6.0
            Genome Coverage                   :: 2536.83088684211x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/14/2023 03:15:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 1,958
            CDSs (total)                      :: 1,869
            Genes (coding)                    :: 1,814
            CDSs (with protein)               :: 1,814
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 55
            CDSs (without protein)            :: 55
            Pseudo Genes (ambiguous residues) :: 0 of 55
            Pseudo Genes (frameshifted)       :: 40 of 55
            Pseudo Genes (incomplete)         :: 18 of 55
            Pseudo Genes (internal stop)      :: 17 of 55
            Pseudo Genes (multiple problems)  :: 14 of 55
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033816.1.
            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..2366
                     /organism="Streptococcus pyogenes"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_514"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_514"
                     /db_xref="taxon:1314"
                     /plasmid="unnamed"
                     /collection_date="2016-01-21"
                     /collected_by="Children's National Hospital"
                     /note="Not specified"
     gene            join(1855..2366,1..223)
                     /gene="erm(C)"
                     /locus_tag="EGX80_RS09965"
                     /old_locus_tag="EGX80_09980"
     CDS             join(1855..2366,1..223)
                     /gene="erm(C)"
                     /locus_tag="EGX80_RS09965"
                     /old_locus_tag="EGX80_09980"
                     /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_001003260.1"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFT
                     LELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPY
                     NISTDIIRKIVFDSIADEIYLIVEYEFAKRLLNTKRSLALFLMAEVDISILSMVPREYF
                     HPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGID
                     DLNNISFEQFLSLFNSYKLFNK"
                     /name="erm(C)"
     gene            671..1147
                     /locus_tag="EGX80_RS09970"
                     /old_locus_tag="EGX80_09985"
     CDS             671..1147
                     /locus_tag="EGX80_RS09970"
                     /old_locus_tag="EGX80_09985"
                     /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             1856..2364
                     /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="98.82"
                     /coverage="69.67"
     ARG             3..223
                     /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="29.92"
     Typing          672..1157
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcacttatc agattaaata gaaaaaaatc aagaatatca cacaaagata aacagaagta
       61 taattatttc gttatgaaat gggttaacaa agaatacaag aaaatattta caaaaaatca
      121 atttaacaat tccttaaaac atgcaggaat tgacgattta aacaatatta gctttgaaca
      181 attcttatct cttttcaata gctataaatt atttaataag taagttaagg gatgcataaa
      241 ctgcatccct taacttgttt ttcgtgtacc tattttttgt gaatcgatta tgtcttttgc
      301 gcattcactt cttttctata taaatatgag cgaagcgaat aagcgtcgga aaagcagcaa
      361 aaagtttcct ttttgctgtt ggagcatggg ggttcagggg gtgcagtatc tgacgtcaat
      421 gccgagcgaa agcgagccga agggtagcat ttacgttaga taaccccctg atatgctccg
      481 acgctttata tagaaaagaa gattcaacta ggtaaaatct taatataggt tgagatgata
      541 aggtttataa ggaatttgtt tgttctaatt tttcactcat tttgttctaa tttcttttaa
      601 caaatgttct ttttttttta gaacagttat gatatagtta gaatagttta aaataaggag
      661 tgagaaaaag atgaaagaaa gatatggaac agtctataaa ggctctcaga ggctcataga
      721 cgaagaaagt ggagaagtca tagaggtaga caagttatac cgtaaacaaa cgtctggtaa
      781 cttcgtaaag gcatatatag tgcaattaat aagtatgtta gatatgattg gcggaaaaaa
      841 acttaaaatc gttaactata tcctagataa tgtccactta agtaacaata caatgatagc
      901 tacaacaaga gaaatagcaa aagctacagg aacaagtcta caaacagtaa taacaacact
      961 taaaatctta gaagaaggaa atattataaa aagaaaaact ggagtattaa tgttaaaccc
     1021 tgaactacta atgagaggcg acgaccaaaa acaaaaatac ctcttactcg aatttgggaa
     1081 ctttgagcaa gaggcaaatg aaaaacaaga aaatgcatta tctgattatt attctttcaa
     1141 ggactagtat aacataaaat cgtctacaaa tagacaaaaa acctgcacgc ttaatgtaga
     1201 tcaaaagctt aacgcaaatg aaatagattg acctcccaat aacaccacgt agttattggg
     1261 aggtcaatct atgaaatgcg attaagcttt ttctaattca cataagcgtg caggtttaaa
     1321 gtacataaaa aatataatga aaaaaagcat cattatacta acgttatacc aacattatac
     1381 tctcattata ctaattgctt attccaattt cctattggtt ggaaccaaca ggcgttagtg
     1441 tgttgttgag ttggtacttt catgggatta atcccatgaa acccccaacc aactcgccaa
     1501 agctttggct aacacacacg ccattccaac caatagtttt ctcggcataa agccatgctc
     1561 tgacgcttaa atgcactaat gccttaaaaa aacattaaag tctaacacac tagacttatt
     1621 tacttcgtaa ttaagtcgtt aaaccgtgtg ctctacgacc aaaagtataa aacctttaag
     1681 aactttcttt tttcttgtaa aaaaagaaac tagataaatc tctcatatct tttattcaat
     1741 aatcgcatca gattgcagta taaatttaac gatcactcat catgttcata tttatcagag
     1801 ctcgtgctat aattatacta attttataag gaggaaaaaa taaagagggt tataatgaac
     1861 gagaaaaata taaaacacag tcaaaacttt attacttcaa aacataatat agataaaata
     1921 atgacaaata taagattaaa tgaacatgat aatatctttg aaatcggctc aggaaaaggg
     1981 cattttaccc ttgaattagt acagaggtgt aatttcgtaa ctgccattga aatagaccat
     2041 aaattatgca aaactacaga aaataaactt gttgatcacg ataatttcca agttttaaac
     2101 aaggatatat tgcagtttaa atttcctaaa aaccaatcct ataaaatatt tggtaatata
     2161 ccttataaca taagtacgga tataatacgc aaaattgttt ttgatagtat agctgatgag
     2221 atttatttaa tcgtggaata cgagtttgct aaaagattat taaatacaaa acgctcattg
     2281 gcattatttt taatggcaga agttgatatt tctatattaa gtatggttcc aagagaatat
     2341 tttcatccta aacctaaagt gaatag
//
