LOCUS       NZ_LS483338             4107 bp    DNA     linear   CON 13-FEB-2024
DEFINITION  Streptococcus pyogenes strain NCTC12064 chromosome 1, complete
            sequence.
ACCESSION   NZ_LS483338 REGION: complement(983954..988060)
VERSION     NZ_LS483338.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3594357
            Assembly: GCF_900475035.1
KEYWORDS    RefSeq.
SOURCE      Streptococcus pyogenes
  ORGANISM  Streptococcus pyogenes
            Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae;
            Streptococcus.
REFERENCE   1
  AUTHORS   Doyle,S.
  CONSRTM   Pathogen Informatics
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUN-2018) WTSI, Pathogen Informatics, Wellcome Trust
            Sanger Institute, CB10 1SA, United Kingdom
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            LS483338.1.
            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/
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/13/2024 01:05:56
            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)                     :: 1,729
            CDSs (total)                      :: 1,640
            Genes (coding)                    :: 1,602
            CDSs (with protein)               :: 1,602
            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)              :: 38
            CDSs (without protein)            :: 38
            Pseudo Genes (ambiguous residues) :: 0 of 38
            Pseudo Genes (frameshifted)       :: 23 of 38
            Pseudo Genes (incomplete)         :: 17 of 38
            Pseudo Genes (internal stop)      :: 15 of 38
            Pseudo Genes (multiple problems)  :: 13 of 38
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4107
                     /organism="Streptococcus pyogenes"
                     /mol_type="genomic DNA"
                     /strain="NCTC12064"
                     /serovar="Lancefield Group A"
                     /isolation_source="not available: to be reported later"
                     /culture_collection="NCTC:12064"
                     /db_xref="taxon:1314"
                     /chromosome="1"
                     /country="United Kingdom: Telford"
                     /collection_date="1900/1982"
     gene            1..4107
                     /gene="cas9"
                     /locus_tag="DQM35_RS05165"
                     /old_locus_tag="NCTC12064_01025"
                     /gene_synonym="csn1"
                     /db_xref="GeneID:69900935"
     CDS             1..4107
                     /gene="cas9"
                     /locus_tag="DQM35_RS05165"
                     /old_locus_tag="NCTC12064_01025"
                     /gene_synonym="csn1"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010922251.1"
                     /GO_component="GO:0005575 - cellular_component [Evidence
                     IEA]"
                     /GO_function="GO:0004520 - DNA endonuclease activity
                     [Evidence IEA]"
                     /GO_process="GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Cas9, originally named Csn1, is the large,
                     multifunctional signature protein of type II CRISPR/Cas
                     systems. It is well known even to general audiences
                     because its RNA-guided endonuclease activity has made it a
                     popular tool for custom editing of eukaryotic genomes.;
                     Cas9, originally named Csn1, is the large, multifunctional
                     signature protein of type II CRISPR/Cas systems. It is
                     well known even to general audiences because its
                     RNA-guided endonuclease activity has made it a popular
                     tool for custom editing of eukaryotic genomes; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II CRISPR RNA-guided endonuclease Cas9"
                     /protein_id="WP_038431314.1"
                     /db_xref="GeneID:69900935"
                     /translation="MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIK
                     KNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLE
                     ESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKADLRLIYLALAH
                     MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASRVDAKAILSARLSK
                     SRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLD
                     NLLAQIGDQYADLFLAAKNLSDATLLSDILRVNSEITKAPLSASMIKRYDEHHQDLTL
                     LKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLAK
                     LNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY
                     YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVL
                     PKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKE
                     DYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLT
                     LFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDF
                     LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQT
                     VKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSDILKE
                     YPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKV
                     LTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKA
                     GFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQF
                     YKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIG
                     KATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLS
                     MPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVV
                     AKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVRKDLIIKLPKYSLF
                     ELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQH
                     KHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA
                     PAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD"
     gene            4107..>4107
                     /gene="cas1"
                     /locus_tag="DQM35_RS05160"
                     /old_locus_tag="NCTC12064_01024"
                     /db_xref="GeneID:69900934"
     CDS             4107..>4107
                     /gene="cas1"
                     /locus_tag="DQM35_RS05160"
                     /old_locus_tag="NCTC12064_01024"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000929484.1"
                     /GO_function="GO:0004520 - DNA endonuclease activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]"
                     /GO_process="GO:0051607 - defense response to virus
                     [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat
                     elements [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II CRISPR-associated endonuclease Cas1"
                     /protein_id="WP_002989953.1"
                     /db_xref="GeneID:69900934"
                     /translation="MAGWRTVVVNTHSKLSYKNNHLIFKDAYKTELIHLSEIDILLLE
                     TTDIVLSTMLVKRLVDENVLVIFCDDKRLPTAMLMPFYGRHDSSLQLGKQMSWSETVK
                     SQVWTTIIAQKILNQSCYLGACSYFEKSQSIMDLYHGLENFDPSNREGHAARIYFNTL
                     FGNDFSRDLEHPINAGLDYGYTLLLSMFAREVVVSGCMTQFGLKHANQFNQFNFASDI
                     MEPFRPLVDKIVYENRNQPFPKIKRELFTLFSDTFSYNGKEMYLTNIISDYTKKVVKA
                     LNNEGKGVPEFRI"
ORIGIN      
        1 atggataaga aatactcaat aggcttagat atcggcacaa atagcgtcgg atgggcggtg
       61 atcactgatg attataaggt tccgtctaaa aagttcaagg ttctgggaaa tacagaccgc
      121 cacagtatca aaaaaaatct tataggggct cttttatttg acagtggaga gacagcggaa
      181 gcgactcgtc tcaaacggac agctcgtaga aggtatacac gtcggaagaa tcgtatttgt
      241 tatctacagg agattttttc aaatgagatg gcgaaagtag atgatagttt ctttcatcga
      301 cttgaagagt cttttttggt ggaagaagac aagaagcatg aacgtcatcc tatttttgga
      361 aatatagtag atgaagttgc ttatcatgag aaatatccaa ctatctatca tctgcgaaaa
      421 aaattggcag attctactga taaagcggat ttgcgcttaa tctatttggc cttagcgcat
      481 atgattaagt ttcgtggtca ttttttgatt gagggagatt taaatcctga taatagtgat
      541 gtggacaaac tatttatcca gttggtacaa acctacaatc aattatttga agaaaaccct
      601 attaacgcaa gtagagtaga tgctaaagcg attctttctg cacgattgag taaatcaaga
      661 cgattagaaa atctcattgc tcagctcccc ggtgagaaga aaaatggatt gtttgggaat
      721 ctcattgctt tgtcattggg attgacccct aattttaaat caaattttga tttggcagaa
      781 gatgctaaat tacagctttc aaaagatact tacgatgatg atttagataa tttattggcg
      841 caaattggag atcaatatgc tgatttgttt ttggcagcta agaatttatc agatgctact
      901 ttactttcag atatcctaag agtaaatagt gaaataacta aggctcccct atcagcttca
      961 atgattaagc gctacgatga acatcatcaa gacttgactc ttttaaaagc tttagttcga
     1021 caacaacttc cagaaaagta taaagaaatc ttttttgatc aatcaaaaaa cggatatgca
     1081 ggttatattg atgggggagc tagccaagaa gaattttata aatttatcaa accaatttta
     1141 gaaaaaatgg atggtactga ggaattattg gcgaaactaa atcgtgaaga tttgctgcgc
     1201 aagcaacgga cctttgacaa cggctctatt ccccatcaaa ttcacttggg tgagctgcat
     1261 gctattttga gaagacaaga agacttttat ccatttttaa aagacaatcg tgagaagatt
     1321 gaaaaaatct tgacttttcg aattccttat tatgttggtc cattggcgcg tggcaatagt
     1381 cgttttgcat ggatgactcg gaagtctgaa gaaacaatta ccccatggaa ttttgaagaa
     1441 gttgtcgata aaggtgcttc agctcaatca tttattgaac gcatgacaaa ctttgataaa
     1501 aatcttccaa atgaaaaagt actaccaaaa catagtttgc tttatgagta ttttacggtt
     1561 tataacgaat tgacaaaggt caaatatgtt actgagggaa tgcgaaaacc agcatttctt
     1621 tcaggtgaac agaagaaagc cattgttgat ttactcttca aaacaaatcg aaaagtaacc
     1681 gttaagcaat taaaagaaga ttatttcaaa aaaatagaat gttttgatag tgttgaaatt
     1741 tcaggagttg aagatagatt taatgcttca ttaggcacct accatgattt gctaaaaatt
     1801 attaaagata aagatttttt ggataatgaa gaaaatgaag atatcttaga ggatattgtt
     1861 ttaacattga ccttatttga agatagggag atgattgagg aaagacttaa aacatatgct
     1921 cacctctttg atgataaggt gatgaaacag cttaaacgtc gccgttatac tggttgggga
     1981 cgtttgtctc gaaaattgat taatggtatt agggataagc aatctggcaa aacaatatta
     2041 gattttttga aatcagatgg ttttgccaat cgcaatttta tgcagctgat ccatgatgat
     2101 agtttgacat ttaaagaaga tattcaaaaa gcacaagtgt ctggacaagg cgatagttta
     2161 catgaacata ttgcaaattt agctggtagc cctgctatta aaaaaggtat tttacagact
     2221 gtaaaagttg ttgatgaatt ggtcaaagta atggggcggc ataagccaga aaatatcgtt
     2281 attgaaatgg cacgtgaaaa tcagacaact caaaagggcc agaaaaattc gcgtgagcgt
     2341 atgaaacgta ttgaagaagg aataaaagaa ctaggaagtg atattctaaa ggagtatcct
     2401 gttgaaaaca ctcaattaca aaatgaaaag ctctatctct attatctcca aaatggaaga
     2461 gacatgtatg tggaccaaga attagatatt aatcgtttaa gtgattatga tgtcgatcac
     2521 attgttccac aaagtttcct taaagacgat tcaatagaca ataaggtctt aacgcgttct
     2581 gataaaaatc gtggtaaatc ggataacgtt ccaagtgaag aagtagtcaa aaagatgaaa
     2641 aactattgga gacaacttct aaacgccaag ttaatcactc aacgtaagtt tgataattta
     2701 acgaaagctg aacgtggagg tttgagtgaa cttgataaag ctggttttat caaacgccaa
     2761 ttggttgaaa ctcgccaaat cactaagcat gtggcacaaa ttttggatag tcgcatgaat
     2821 actaaatacg atgaaaatga taaacttatt cgagaggtta aagtgattac cttaaaatct
     2881 aaattagttt ctgacttccg aaaagatttc caattctata aagtacgtga gattaacaat
     2941 taccatcatg cccatgatgc gtatcttaat gccgtcgttg gaactgcttt gattaagaaa
     3001 tatccaaaac ttgaatcgga gtttgtctat ggtgattata aagtttatga tgttcgtaaa
     3061 atgattgcta agtctgagca ggaaataggc aaagcaaccg caaaatattt cttttactct
     3121 aatatcatga acttcttcaa aacagaaatt acacttgcaa atggagagat tcgcaaacgc
     3181 cctctaatcg aaactaatgg ggaaactgga gaaattgtct gggataaagg gcgagatttt
     3241 gccacagtgc gcaaagtatt gtccatgccc caagtcaata ttgtcaagaa aacagaagta
     3301 cagacaggcg gattctccaa ggagtcaatt ttaccaaaaa gaaattcgga caagcttatt
     3361 gctcgtaaaa aagactggga tccaaaaaaa tatggtggtt ttgatagtcc aacggtagct
     3421 tattcagtcc tagtggttgc taaggtggaa aaagggaaat cgaagaagtt aaaatccgtt
     3481 aaagagttac tagggatcac aattatggaa agaagttcct ttgaaaaaaa tccgattgac
     3541 tttttagaag ctaaaggata taaggaagtt agaaaagatt taatcattaa actacctaaa
     3601 tatagtcttt ttgagttaga aaacggtcgt aaacggatgc tggctagcgc cggggaattg
     3661 caaaaaggaa atgagctggc tctgccaagc aaatatgtga attttttata tttagctagt
     3721 cattatgaaa agttgaaggg tagtccagaa gataacgaac aaaaacaatt gtttgtggag
     3781 cagcataagc attatttaga tgagattatt gagcaaatca gtgaattttc taagcgtgtt
     3841 attttagcag atgccaattt agataaagtt cttagtgcat ataacaaaca tagagacaaa
     3901 ccaatacgtg aacaagcaga aaatattatt catttattta cgttgacgaa tcttggagct
     3961 cccgctgctt ttaaatattt tgatacaaca attgatcgta aacgatatac gtctacaaaa
     4021 gaagttttag atgccactct tatccatcaa tccattactg gtctttatga aacacgcatt
     4081 gatttgagtc agctaggagg tgactga
//
