LOCUS       NZ_CMIW01000017         5549 bp    DNA     linear   CON 27-NOV-2024
DEFINITION  Streptococcus pneumoniae strain SMRU3003, whole genome shotgun
            sequence.
ACCESSION   NZ_CMIW01000017
VERSION     NZ_CMIW01000017.1
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_001092805.1-RS_2024_11_27
            Annotation Date                   :: 11/27/2024 00:58:22
            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)                     :: 2,159
            CDSs (total)                      :: 2,109
            Genes (coding)                    :: 1,938
            CDSs (with protein)               :: 1,938
            Genes (RNA)                       :: 50
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 44
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 171
            CDSs (without protein)            :: 171
            Pseudo Genes (ambiguous residues) :: 0 of 171
            Pseudo Genes (frameshifted)       :: 69 of 171
            Pseudo Genes (incomplete)         :: 100 of 171
            Pseudo Genes (internal stop)      :: 55 of 171
            Pseudo Genes (multiple problems)  :: 44 of 171
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 09:52:54
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 34925
            Orig. end                         :: 40474
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CMIW01000017.1.
            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
     region          1..5549
                     /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..5549
                     /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..5549
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[5000:5300](-)"
                     /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(5001..5300)
                     /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"
     misc_feature    406..420
                     /note="TFBS match to VqsM, Regulator of quorum-sensing
                     signalling systems, confidence: weak, score: 16.66"
                     /tool="antismash"
     gene            complement(810..2162)
                     /gene="murD"
                     /locus_tag="AD046_RS09925"
                     /old_locus_tag="ERS022513_01951"
     CDS             complement(810..2162)
                     /EC_number="6.3.2.9"
                     /GO_component="GO:0005737 - cytoplasm [Evidence IEA]"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /GO_function="GO:0008764 -
                     UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
                     [Evidence IEA]"
                     /GO_process="GO:0008360 - regulation of cell shape
                     [Evidence IEA]"
                     /GO_process="GO:0009252 - peptidoglycan biosynthetic
                     process [Evidence IEA]"
                     /GO_process="GO:0051301 - cell division [Evidence IEA]"
                     /codon_start=1
                     /gene="murD"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000862950.1"
                     /locus_tag="AD046_RS09925"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS022513_01951"
                     /product="UDP-N-acetylmuramoyl-L-alanine--D-glutamate
                     ligase"
                     /protein_id="WP_050116264.1"
                     /transl_table=11
                     /translation="MKVIDQLKNKKVLVLGLAKSGESAARLLDKLGAIVTVNDGKPFED
                     NPAAQSLLEEGIKVITGGHPLELLDEEFALMVKNPGIPYNNPMIEKALAKGIPVLTEVE
                     LAYLISEAPIIGITGSNGKTTTTTMIGEVLTAAGQHGLLSGNIGYPASQVAQIASDKDT
                     LVMELSSFQLMGVQEFHPEIAVITNLMPTHIDYHGSFSEYVAAKWNIQNKMTAADFLVL
                     NFNQDLAKDLTSKTEATVVPFSTLEKVDGAYLEDGQLYFRGEVVMAANEIGVPGSHNVE
                     NALATIAVAKLRGVDNQTIKETLSAFGGVKHRLQFVDDIKGVKFYNDSKSTNILATQKA
                     LSGFDNSKVVLIAGGLDRGNEFDELVPDITGLKKMVILGQSAERVKRAADKAGVAYVEV
                     TDIADATRKAYELATQGDVVLLSPANASWDMYANFEVRGDLFIDTVAELKE"
     gene            complement(2266..2907)
                     /locus_tag="AD046_RS09930"
                     /old_locus_tag="ERS022513_01952"
     CDS             complement(2266..2907)
                     /codon_start=1
                     /gene_functions="transport (smcogs) SMCOG1000: ABC
                     transporter ATP-binding protein"
                     /gene_kind="transport"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000571297.1"
                     /locus_tag="AD046_RS09930"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS022513_01952"
                     /product="ABC transporter ATP-binding protein"
                     /protein_id="WP_000571281.1"
                     /transl_table=11
                     /translation="MIELKNISKKFGSRQLFSDTNLHFEGGKIYALIGTSGCGKTTLLN
                     MIGRLEPYDKGQIIYDGTSLKDIKPSVFFRDYLGYLFQDFGLIESQTVKENLNLGLVGK
                     KLKEKEKISLMKQALNCVNLSYLDLKQPIFELSGGEAQRVALAKIILKDPPLILADEPT
                     ASLDPKNSEELLSILESLKNPNRTIIIATHNPLIWEQVDQVIRVTDLSHR"
     gene            complement(2909..4930)
                     /locus_tag="AD046_RS09935"
                     /old_locus_tag="ERS022513_01953"
     CDS             complement(2909..4930)
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000732428.1"
                     /locus_tag="AD046_RS09935"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS022513_01953"
                     /product="bacteriocin-associated integral membrane family
                     protein"
                     /protein_id="WP_000732439.1"
                     /transl_table=11
                     /translation="MKKLFILLSTFFLSFFLAWIIVLRAPQYLYASYDSVSLLRVKKDT
                     QEPTREVFEQELENFANSEQSLIVRRIVEPSKDGTTHFTYATYGQGTLPKEFQEASQES
                     RERSDPLNSYLLLSGSLTKEKLADKLGDLGYKASADRKIPPYFLAFRILLNPLILISLA
                     IFGLSFFALVIITRIKEMRAAGIKLFSGQTLLSIMGHSLSTDIKWLLLSALLSFLGGGV
                     VLFSQGLFYPILLATYGFGISFYLLFLLAISILLMLLYLMSLNYKALVPVIKERLPLKR
                     LMILTLLCQLVAVFTVGYAVKTGLTSYQRLKELEISKQAWQDRADYYQISFGLGDRGKD
                     TENQSKWYAFAKEAIEEEQALYVKDNLLHFANPQGKNEQGETLDTYSPDANTLYVSPSY
                     LDKEKVVVDAETKQKLAHLQKGEFILLLPEHLRSREAELKKVFEERLSYYGKSGEEASA
                     PLDYEMKAHVSYLSMGEKRFVYNNGENPVSTQYLTDPILVVFTPTSTGDSFISLSSWSI
                     NAGKQLFIKGYESGLELLKKAGIYEQVSYLKEGRSVYLTRYNEVQTETATLILGAIVGI
                     ASSLLLFYSVNLLYFEQFRRDILIKRISGLRFFETHAQYMVSQFASFVFGASLFILSSR
                     DLVIGLLTLLVFLASAVLTLYRQAQKESRVSMTIMKGK"
     gene            complement(5001..5300)
                     /locus_tag="AD046_RS09940"
                     /old_locus_tag="ERS022513_01954"
     CDS             complement(5001..5300)
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters)
                     RiPP-like: Lactococcin_972"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016397967.1"
                     /locus_tag="AD046_RS09940"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS022513_01954"
                     /product="lactococcin 972 family bacteriocin"
                     /protein_id="WP_000850391.1"
                     /sec_met_domain="Lactococcin_972 (E-value: 4.9e-29,
                     bitscore: 92.3, seeds: 6, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MKTKKHRLLALVLISSFTLLGAASAAVQYPDGGVWTYGEGSGGGW
                     AFSNYYHGKKYHYSSIVSRWDGHSDKGEAPAGKTSYAWIWTKWGEQVAFYCDYD"
     misc_feature    complement(5389..5404)
                     /note="TFBS match to CRP, Cyclic AMP receptor protein,
                     confidence: medium, score: 17.55"
                     /tool="antismash"
ORIGIN
        1 ctatcgccaa gagctcaaaa atcgtattgg caccacctcg tgtcacaaca atatcagcca
       61 attccatcaa gggttgatag agatcggtca catagtcaac acgaaaaaga ttttgcctca
      121 actcattcag actagaatct ccagttagat tgataatatt gtagcgctct gttagttctt
      181 tcttatggtc tgtcaccaat tggttaaaga cacgagcgcc tgcagaaccg ccgacaaaca
      241 atacagttgg caatttggga ttaaagtggg tttgaatatc caccaattca tctggttctg
      301 gagtgttttt gtccgaaacc ttggtcaccg ctcccacatg ctcaacctta gccaaactcg
      361 aagcttgttc aaaggttgaa tacatcttag tcgcaaattt ataggcgatt ttattggcca
      421 agcccataga caggtcagat tcgtgaataa agacaggcac tcctgacaca cgcgctgcga
      481 taacaggcgg tactgagaca aagcccccct ttgaaaaaag ggtctgtgga cgaagtcgca
      541 acatgataaa gagcgattgg acgattcccc agccaacttt gaagacgtcc agcatatttt
      601 gccaagagaa atagcgacgc aatttcccag tcgcaatgga gtggaaagtg acatccaaac
      661 ctgacttaag gatttcttgg tgttcgatac cacgcttgtc cccgatatag tggacttccc
      721 aaccatcttc gatgaacttg ggcattaaca aaagattgag ggtaacgtgt ccaaccgtcc
      781 ccccacctgt aaagacaatt tttttcatat tattctttta actccgctac tgtgtcgata
      841 aagaggtcgc cacgtacttc aaagttagca tacatatccc agctggcatt ggcaggacta
      901 agaagaacca catctccttg agtcgcaagc tcataggcct tgcgggtcgc atctgcaata
      961 tctgtcacct ccacataagc gacaccagcc ttgtctgctg cccgtttgac acgttctgca
     1021 gattgaccca ggatgaccat cttcttgagt ccagtaatgt ctggcaccaa ttcgtcaaac
     1081 tcattgccac ggtccaaacc acctgcaatc aagacgacct tgctgttgtc aaatcctgat
     1141 aaggcttttt gagtagccaa gatattagtt gatttactgt cgttatagaa tttaacaccc
     1201 ttgatgtcat ccacaaactg gagacggtgt ttgacaccac cgaaggctga aagagtttcc
     1261 ttgatggttt gattgtccac accacgaagc ttggctacag caatagtcgc aagggcattt
     1321 tccacattgt ggctacctgg aacaccgatt tcattcgctg ccatgactac ttcaccacgg
     1381 aagtagagtt gaccatcttc cagataagct ccatcaacct tttcaagtgt tgaaaatggt
     1441 acaacagtgg cttctgtctt ggaagtcaag tcttttgcca agtcttgatt aaagttcaag
     1501 acaaggaaat cagctgctgt catcttgttc tggatattcc acttggctgc tacatattcc
     1561 gaaaatgacc catggtagtc gatatgagtt ggcatgaggt tggtaataac cgcaatctct
     1621 ggatggaatt cttgaacacc catgagttgg aaagaagaaa gttccataac aagcgtgtcc
     1681 ttatctgatg ctatttgagc aacctgacta gctggatagc cgatattccc tgataaaaga
     1741 ccatgttgcc cagcagcagt caaaacttcc ccaatcatag tcgttgtggt tgtcttaccg
     1801 ttcgatcctg tgataccaat aatcggtgct tctgaaatca aataagccaa ttccacctca
     1861 gtcaagactg gaattccctt ggccaaagcc ttttcaatca tgggattgtt gtaggggata
     1921 cctggatttt tcaccataag ggcaaactct tcatccaaga gttccaaagg atggccacct
     1981 gtaatgacct tgatcccttc ttccagcaaa ctttgggcag ctggattgtc ctcgaaaggt
     2041 ttcccatcat ttactgtcac aatggcacct agcttgtcca acaaacgagc tgcagattca
     2101 ccagacttgg ccaaacctaa aacaaggact ttcttatttt ttaattgatc tattactttc
     2161 atgtctcgaa ctccatttct actcctacta ttttaccatt tttatggaaa taaaaaagcc
     2221 acaaagtgtg tttgtgactc tttcttctaa ctgaatctta ccatatcatc tatgtgataa
     2281 atcggtaact cgaatgacct gatccacttg ttcccaaata agaggattgt gggtcgcaat
     2341 aataatggtc cgattcggat tttttaaaga ttctaggatg gaaagtaatt cctcagagtt
     2401 tttggggtct aaggaagcgg ttggttcatc tgcgaggatc aaaggtggat cctttaaaat
     2461 tatcttcgct aatgcaacac gttgtgcttc tcctcctgat aactcaaata taggttgctt
     2521 caaatccaaa taagagaggt ttacacagtt tagagcttgt ttcatcaaag agattttctc
     2581 tttttccttc aactttttac caactaaacc cagattgaga ttctctttga cggtttggct
     2641 ttcaattaag ccaaaatctt gaaataagta tcctaagtaa tctctaaaga aaacagaagg
     2701 cttgatgtcc ttaagagaag tgccatcata gatgatttgc cctttgtcat atggctctaa
     2761 tcgtccaatc atattcaaga gtgttgtctt accacagcca cttgtaccga ttaaggcata
     2821 aattttccca ccttcaaaat gaagatttgt atctgaaaat agctgacggc ttccaaattt
     2881 tttagatata ttctttagtt caatcatcct attttccttt cataattgtc atagaaacac
     2941 gagattcttt ctgtgcttga cggtaaagcg tcagaactgc actagctaga aagactaata
     3001 aagtgagcaa gccaatcacc aagtctcgac tgcttaaaat aaagagacta gcaccaaata
     3061 caaaactggc aaattgacta accatatact gagcatgtgt ttcaaaaaat cgtaaacctg
     3121 aaattcgttt aatcaaaata tctcggcgga attgctcgaa atatagaaga ttgacagaat
     3181 aaaatagtaa caaggaacta gctatcccca caatagctcc taagattaaa gttgctgttt
     3241 cagtttgaac ttcattataa cgagttagat aaacacttct tccttcttta agataggaca
     3301 cttgctcata aattccagct ttcttcaaga gttctagccc actctcatat cctttgataa
     3361 agagttgttt tccagcattg atagaccaac tagataagga tataaaacta tcacctgtag
     3421 aagtcggcgt gaataccact aaaatcggat cagtcaaata ctgagtggat acgggattct
     3481 caccgttatt ataaacaaac cgcttttctc ccattgaaag ataactaacg tgcgctttca
     3541 tctcataatc caaaggagca cttgcctcct caccagattt tccataataa ctcaatcttt
     3601 cttcaaaaac tttcttaagt tctgcttctc gagagcgcaa atgttctggg agcaagagga
     3661 taaactcacc tttttggaga tgggctaact tctgtttggt ctcagcatct accacgacct
     3721 tttccttgtc caaataactg ggactaacat agagcgtatt agcatctgga ctataggtat
     3781 ccagtgtctc tccctgttca ttttttcctt gtggattggc aaaatggagc agattatcct
     3841 ttacataaag agcttgttct tcttcgattg cttctttggc aaaggcatac cacttgctct
     3901 gattttctgt atcttttcct ctatcaccta agccaaaaga aatttgataa tagtctgctc
     3961 tatcctgcca tgcttgtttt gaaatttcaa gttctttcaa tcgttggtaa gacgtcaaac
     4021 ctgtcttaac agcgtatcct actgtaaaga cagcaaccaa ctgacacaat agggttaaaa
     4081 tcatcaggcg tttaaggggt aatctctcct taataacggg aactaatgct ttgtaattca
     4141 aactcattag ataaagaagc attagtaaaa ttgaaatcgc caataaaaac aacagataga
     4201 aactaatccc aaaaccatag gtggctaaca agataggata aaacaaacct tgactaaaaa
     4261 gaacgactcc cccacctagg aaggaaagga gggctgatag aaggagccat ttgatatcag
     4321 tagataaaga atgccccatg atggataaga gagtctgacc agaaaagagt tttatacctg
     4381 ctgctctcat ttccttaatc cgagtgataa tcactaaagc aaagaaagat aagccaaata
     4441 ttgctaaact aattaaaata aggggattta gtaatattcg aaaagcaaga aaatagggcg
     4501 gtatctttcg gtcagcactt gctttataac ccaaatctcc taatttatcg gcaagctttt
     4561 ctttcgtcaa ggagcctgac aaaaggagat aactatttag cggatcacta cgttcacgac
     4621 tttcttggct agcttcttgg aattcttttg gtaaagttcc ctgaccataa gttgcataag
     4681 taaagtgagt cgtcccatcc ttactcggct ctacaattct tctaactatt aaactctgtt
     4741 ctgagtttgc aaaattctcc aattcctgtt caaatacctc acgcgtcggt tcctgagtat
     4801 cttttttgac acgaagtaaa gaaacggaat catagcttgc atataaatat tgtggcgcac
     4861 gtaagacaat aatccaagca aggaagaagc tgagaaaaaa agttgataat aatatgaata
     4921 gtttcttcat agtagactcc ttgtaaacaa aattccccct gtaatttctt acaaggggaa
     4981 cgatttaaat caatgaacga ttagtcataa tcacagtaaa atgctacttg ttctccccat
     5041 ttagtccaaa tccatgcata ggaggttttt ccagcaggag cttctccttt atcagaatga
     5101 ccatcccatc tgctcacgat ggatgaataa tgatattttt taccatgata gtaatttgaa
     5161 aaagcccaac cacctcctga accttctcca tatgtccata ctcctccatc tggatattgt
     5221 acagcagctg atgcagctcc caataatgta aaacttgaaa taagaactag agcaagtaat
     5281 ctatgttttt tcgttttcat tttatttttt ctttcaaaaa aagcacacct tgagcaacaa
     5341 tgcaacaaaa taaaccctcc tctttctttt gttgaaaccg ctttcttatg tgatgagaat
     5401 aacattttta ttatttgttg tcaaggaaaa aatcgaattt tttagatatt ttactatatt
     5461 acctctatga atgaaagttc tataatgaag ttagccacct taccttagtc aagaattaga
     5521 tgtttcacta tgtttgagta agttgatga
//
