LOCUS       NZ_CRAW01000040         4203 bp    DNA     linear   CON 12-DEC-2024
DEFINITION  Streptococcus pneumoniae strain SMRU702, whole genome shotgun
            sequence.
ACCESSION   NZ_CRAW01000040
VERSION     NZ_CRAW01000040.1
KEYWORDS    WGS; RefSeq.
SOURCE      Streptococcus pneumoniae
  ORGANISM  Streptococcus pneumoniae
            Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales;
            Streptococcaceae; Streptococcus.
REFERENCE   1
  AUTHORS   Informatics,Pathogen.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAR-2015) SC, Wellcome Trust Sanger Institute, CB10
            1SA, United Kingdom
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001193635.1-RS_2024_12_12
            Annotation Date                   :: 12/12/2024 01:34:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,202
            CDSs (total)                      :: 2,158
            Genes (coding)                    :: 1,981
            CDSs (with protein)               :: 1,981
            Genes (RNA)                       :: 44
            rRNAs                             :: 2, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 37
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 66 of 177
            Pseudo Genes (incomplete)         :: 114 of 177
            Pseudo Genes (internal stop)      :: 46 of 177
            Pseudo Genes (multiple problems)  :: 43 of 177
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 03:02:04
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 4203
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CRAW01000040.1.
            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/
FEATURES             Location/Qualifiers
     gene            complement(<1..573)
                     /locus_tag="AK725_RS10820"
     CDS             complement(<1..573)
                     /EC_number="3.4.-.-"
                     /codon_start=1
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) Abi"
                     /gene_kind="biosynthetic-additional"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000394041.1"
                     /locus_tag="AK725_RS10820"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="CPBP family intramembrane glutamic endopeptidase"
                     /protein_id="WP_050967384.1"
                     /sec_met_domain="Abi (E-value: 6.6e-12, bitscore: 34.7,
                     seeds: 823, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MEFFDKFHALCFGFLVLIIVITVPYTINHGGFFQNESALILVSLL
                     VTSLSVAYARKFEMISFGMLSKKQLLLFIAIFLLSVLETLVYIHFFAVSSGSGVQHLAE
                     VSRGISLSLILTTSVFGPIQEELIFRGLLQGAVFDNSWLGLVLTSSLFSFMHGPSNVPS
                     FIFYPNHSYLSQLDVTYKTPDLMSHFLP"
     source          1..4203
                     /collection_date="2008-08-29"
                     /db_xref="taxon:1313"
                     /geo_loc_name="Thailand:Maela"
                     /host="Homo sapiens"
                     /isolation_source="nasopharynx"
                     /mol_type="genomic DNA"
                     /organism="Streptococcus pneumoniae"
                     /serovar="17F"
                     /strain="SMRU702"
     region          1..4203
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="RiPP-like"
                     /region_number="1"
                     /rules="(strepbact or Antimicrobial14 or Bacteriocin_IId or
                     BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or
                     Lactococcin or Antimicrobial17 or Lactococcin_972 or
                     Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or
                     TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or
                     TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))"
                     /tool="antismash"
     cand_cluster    1..4203
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="(strepbact or Antimicrobial14 or
                     Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or
                     Bacteriocin_IIi or Lactococcin or Antimicrobial17 or
                     Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin
                     or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or
                     TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or
                     TIGR03604))"
                     /kind="single"
                     /product="RiPP-like"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..4203
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[3712:3943](-)"
                     /cutoff="20000"
                     /detection_rule="(strepbact or Antimicrobial14 or
                     Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or
                     Bacteriocin_IIi or Lactococcin or Antimicrobial17 or
                     Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin
                     or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or
                     TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or
                     TIGR03604))"
                     /neighbourhood="5000"
                     /product="RiPP-like"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      complement(3713..3943)
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="(strepbact or Antimicrobial14 or
                     Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or
                     Bacteriocin_IIi or Lactococcin or Antimicrobial17 or
                     Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin
                     or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or
                     TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or
                     TIGR03604))"
                     /neighbourhood="5000"
                     /product="RiPP-like"
                     /protocluster_number="1"
     gene            complement(724..957)
                     /gene="blpZ"
                     /locus_tag="AK725_RS10825"
                     /old_locus_tag="ERS020212_02106"
     CDS             complement(724..957)
                     /codon_start=1
                     /gene="blpZ"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000276505.1"
                     /locus_tag="AK725_RS10825"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS020212_02106"
                     /product="immunity protein BlpZ"
                     /protein_id="WP_000276498.1"
                     /transl_table=11
                     /translation="MYKHLFFLDSKTLDRLTPYILVLASDTIAFNVFVLTFVSAVVFNF
                     LNSMLALMAIFIGAGYVVGFWLLILNENQRAN"
     gene            complement(999..1688)
                     /locus_tag="AK725_RS10830"
                     /old_locus_tag="ERS020212_02107"
     CDS             complement(999..1688)
                     /EC_number="3.4.-.-"
                     /codon_start=1
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) Abi"
                     /gene_kind="biosynthetic-additional"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000760553.1"
                     /locus_tag="AK725_RS10830"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS020212_02107"
                     /product="CPBP family intramembrane glutamic endopeptidase"
                     /protein_id="WP_000760532.1"
                     /sec_met_domain="Abi (E-value: 6.3e-15, bitscore: 44.4,
                     seeds: 823, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MKKYQLLFKISAVFSYLFFVFGLSQMTLIIQNYWQFSSQIGNFVW
                     IQNFLSLLFSGVMIWILVKTGHGYLFHIPRKKWLWYSILTVLVVVLQISFNVQTAKHVQ
                     STAEGWAVLIGYSGTNFAELGIYITLFFLTPLMEELIYRGLLQHAFFKHSRFGLDLLLP
                     SILFALPHFSSLPSLLDIFIFATSGIIFASLTRYTKSIYPSYAVHVINNIFATLPFLLT
                     FLHRVLG"
     gene            complement(1740..2123)
                     /locus_tag="AK725_RS10835"
                     /old_locus_tag="ERS020212_02108"
     CDS             complement(1740..2123)
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016398494.1"
                     /locus_tag="AK725_RS10835"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS020212_02108"
                     /product="hypothetical protein"
                     /protein_id="WP_000877381.1"
                     /transl_table=11
                     /translation="MKYRLFFVIFLSSVLDILLGTFLQISIVSIGWLVLYSGLFEAGVF
                     LLANKGVAVKIKEVDIRNRFKFIFGKTLWFQILLLIFLIIKLYLGLDARLILFYGHIFI
                     VFNALMYLLSSSQVSLKKNKLSS"
     gene            complement(2752..3110)
                     /locus_tag="AK725_RS10845"
                     /old_locus_tag="ERS020212_02109"
                     /pseudo=""
     CDS             complement(2752..3110)
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000846948.1"
                     /locus_tag="AK725_RS10845"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /old_locus_tag="ERS020212_02109"
                     /product="immunity protein"
                     /pseudo=""
                     /transl_table=11
                     /translation="MIFFVRLFLGQLPLLVSTYLFLFRQFSNFF"
     misc_feature    3442..3455
                     /note="TFBS match to LexA_variant_2, Repressor of DNA
                     damage response, confidence: medium, score: 20.08"
                     /tool="antismash"
     gene            complement(3591..3710)
                     /locus_tag="AK725_RS10850"
     CDS             complement(3591..3710)
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000346296.1"
                     /locus_tag="AK725_RS10850"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="PncF family bacteriocin immunity protein"
                     /protein_id="WP_000346296.1"
                     /transl_table=11
                     /translation="MDFKSFIIGLVVGIFGPYMDDLIRKIFSKSSKKDTDSTL"
     gene            complement(3713..3943)
                     /gene="blpU"
                     /locus_tag="AK725_RS10855"
                     /old_locus_tag="ERS020212_02111"
     CDS             complement(3713..3943)
                     /codon_start=1
                     /gene="blpU"
                     /gene_functions="biosynthetic (rule-based-clusters)
                     RiPP-like: Bacteriocin_IIc"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001093487.1"
                     /locus_tag="AK725_RS10855"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS020212_02111"
                     /product="bacteriocin-like peptide BlpU"
                     /protein_id="WP_001093075.1"
                     /sec_met_domain="Bacteriocin_IIc (E-value: 2e-18, bitscore:
                     55.5, seeds: 35, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MNTKKMSQFEIMDTEMLACVEGGGCNWGDFAKAGVGGGAVRGLQL
                     GIKTRTWQGAATGAAGGAILGGVAYAATCWW"
ORIGIN
        1 aggaagaaag tggctcatga ggtcaggggt tttgtaagtt acatctagtt gagagaggta
       61 tgaatgattt gggtaaaaaa taaacgaagg gacattagaa ggtccatgca tgaaagaaaa
      121 gagagaggaa gttagcacaa gccctaacca agaattgtca aaaaccgcac cttgaagaag
      181 tcctctgaaa atgagttcct cctggatggg gccaaaaact gaggtagtca aaatcaaaga
      241 cagggaaatt cctctgctga cttccgccaa gtgttggacc cctgagccag aagaaacagc
      301 gaagaaatga atataaacca gcgtctcaag tacacttaga agaaagattg caatgaaaag
      361 caaaagttgt ttcttgctta acatcccaaa agaaatcatt tcaaactttc tagcataagc
      421 aacactcagc gaggttacaa gaagacttac aagaatcaat gcagattcat tttgaaaaaa
      481 acccccatgg ttaatcgtat aaggaactgt aatgacaatt attagtacta aaaatccaaa
      541 acacaaggca tgaaatttat caaaaaactc cataaaacta tcctcctcac caaacagact
      601 tcctacgcgt cattctttag ttctagcctt tccaaaacaa accattttat actcttcgaa
      661 aatcaaattc aaaccacgtc aacgtcgcct tgccgtactc aagtacagcc tgcggctagt
      721 ttcctagttt gctctttgat tttcattgag tattagtaac caaaatccga ccacatagcc
      781 agcccctatg aatatagcca ttaaagctag catggaattt aggaaattaa aaaccaccgc
      841 agatacaaag gttagcacaa aaacattaaa agcaatggtg tcagaagcca agactagaat
      901 atagggtgtc aaccgatcta aagttttgga atctaggaaa aataagtgtt tatacatgat
      961 aatctcctct atggctgaaa agcaagcctt ttgttttttt accccaagac cctatgtaaa
     1021 aaagtcagca aaaatggtaa tgttgcgaaa atattattga tcacatgcac cgcataggaa
     1081 ggataaatgc tcttggtata gcgggtcaaa ctagcaaaga tgatgccaga tgttgcaaag
     1141 atgaagatat ctaacaaact aggcaggctt gaaaaatgag gaagagcaaa taaaattgac
     1201 ggaagaagca aatcaaggcc aaatctcgaa tgcttaaaaa aggcgtgttg cagtaatcct
     1261 ctatagatta gctcttccat aagtggagtc agaaagaaca aagttatata gatacctagc
     1321 tcagcaaagt tggtcccact ataaccgatc aatacagccc aaccttcagc agttgactga
     1381 acatgtttag ctgtctgaac gttaaaagag atctggagca ctaccactaa tactgtcaaa
     1441 atcgaatacc aaagccattt ttttcttgga atgtgaaaga gataaccatg acctgtctta
     1501 accagaatcc aaatcatgac tccgctaaat agcaaactca agaaattttg aatccagacg
     1561 aaattgccaa tctgggaaga aaattgccaa taattttgaa taataagcgt catctgagaa
     1621 agaccaaata cgaaaaataa gtaagagaaa actgcactta ttttgaatag aagttgatac
     1681 tttttcatag aaatcctccc tactatgacc tcaccttgtc aggctctact gctgtaagat
     1741 taagaagaca gtttgttttt tttaaggcta acctgactac tagataatag atacattaag
     1801 gcattaaaga caatgaaaat atgtccatag aataaaatca acctcgcatc caaaccaaga
     1861 taaagtttga ttatcaaaaa gatgagcaaa agaatttgaa accataaggt ttttccaaaa
     1921 ataaatttaa agcgatttcg aatatctact tccttgattt ttaccgccac ccctttatta
     1981 gcaagaagga aaactcctgc ttcaaacaaa ccactgtaaa gaacaagcca cccaatagat
     2041 acgatagaga tttgtaaaaa tgtccctaaa agaatatcca acacactact caagaaaata
     2101 acaaaaaata atctgtattt catattaaat acctccattc atttatttca ctaacaattt
     2161 aatagagcct tctactcaaa tatcctgtca gaaaaggata gaaagctact ttttataata
     2221 cttcaagccc cacatgagca gaagcgtgat aaacaagcag agaatacacc tatataagcg
     2281 attagttgtt gatagaattc tgtttctgaa atacctctat acaaacaaat gacaaacata
     2341 aaatctgcca agccgataaa cataagttga ttggttctag gactaaccaa atcatcattt
     2401 acttatattt aagagtatct cttttatgtt aatgtatgtt agcactgaaa agcaagacag
     2461 gccaataata tttaaaatga acagtaacgg ggttaagtct ctaaaaaaat tatctactga
     2521 cactacaaga aatactatac atattatagt cgaaactatc tttttcttat ccataattat
     2581 ttactccttt cctaacaaat ccaacttatc aatcaagagc gatttttaac ataatgtagc
     2641 agcacccgtt gcaactttga caagtttagt atatcattgt tttttaaaat ttttcatcca
     2701 aatcttgaat tgtcatcgaa acctcctaaa ttgcaaaaac ttcattagcc cctacttttt
     2761 ataatacttc aaaccccaaa tgagtagaag catgatgatc aagcaaagaa tagcaccaat
     2821 ataagcgatt agttgttgat aagattctcc tgctgtgata cctctataca aacaaataat
     2881 agacataaag cctgtcaagc cgataaacat gagttgattg gttctaggac taaccaaatc
     2941 atcatcttca aactctctta atctcatttc cctagtaaga taaacagtaa ccaaaataga
     3001 agtcaagtta ataactacta aaagaaattg gaaaactgac gaaatagaaa tagataagta
     3061 gaaacaagca aaggcaactg acccaggaac aatctcacaa agaatatgat tctttttaat
     3121 caagaaaatc tttcatttct tttctttctt tttaattaaa gaaaaataga tcataaccgc
     3181 aatcatatag gctatggtat aaaatagatt ataccaaata ctctccctaa gcggataaag
     3241 aaagatggac atgatcagat acagaacgaa aataatcagt atttttttct tcataagttt
     3301 tcctcctaaa tgtgcgattt atcttagttg agcaagaaca tttacactgc tagtatagca
     3361 cttattttga ccttggatca ctcaaatcat aaatggtcat caaaacctct tgaattgtaa
     3421 aaattaaaaa agcaagcatg aaaaacatac tttcctcttt atattgtatt gataccaact
     3481 tgtttgtaga cttttcatcc tgctatcaca tatcattttg acaggcgaaa caatattaaa
     3541 gaaactcccc tgtaaattaa gctagcaaat acaggggaga aatttatttt ttagagagta
     3601 ctatccgtat cctttttgga agattttgaa aatatttttc taattaagtc atccatataa
     3661 ggaccaaata taccaactac taaaccaata ataaaacttt taaaatccat aattaccacc
     3721 aacatgtcgc tgcataggcc acacctccaa gtatagctcc tcccgcagca ccagttgctg
     3781 caccttgcca tgttcttgtt ttaattccta gctgaagacc tcgtactgct cctcctccaa
     3841 cacctgcttt ggcaaaatct ccccaattgc atccgccacc ttcaacgcaa gcaagcatct
     3901 cagtatccat aatttcaaat tgtgacatct tttttgtatt cataacgaat acctcttttt
     3961 tatttttaat atttgtcttg ttacaaactt gacaagttta gtataacagt atctattaat
     4021 ttttttcatc caaatcttga attggcatcg aaacgtcttg aattagcttt tttgtttcaa
     4081 aatcatctct atttttaaaa aagatgtttt ctaatcactt ttttactatt agacttcctg
     4141 caaaactaga atcctagttc atgattgata ataccagcaa tcaaattcat tcgtaatccg
     4201 aag
//
