LOCUS       NZ_FEEQ01000029         5337 bp    DNA     linear   CON 04-JAN-2025
DEFINITION  Streptococcus pneumoniae strain 2842STDY5644069, whole genome
            shotgun sequence.
ACCESSION   NZ_FEEQ01000029
VERSION     NZ_FEEQ01000029.1
KEYWORDS    WGS; RefSeq.
SOURCE      Streptococcus pneumoniae
  ORGANISM  Streptococcus pneumoniae
            Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales;
            Streptococcaceae; Streptococcus.
REFERENCE   1
  CONSRTM   Pathogen Informatics
  TITLE     Direct Submission
  JOURNAL   Submitted (04-FEB-2016) SC, Wellcome Trust Sanger Institute, CB10
            1SA, United Kingdom
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_900047005.1-RS_2025_01_04
            Annotation Date                   :: 01/04/2025 01:43:28
            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)                     :: 2,253
            CDSs (total)                      :: 2,202
            Genes (coding)                    :: 2,019
            CDSs (with protein)               :: 2,019
            Genes (RNA)                       :: 51
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 45
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 184
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 184
            Pseudo Genes (frameshifted)       :: 86 of 184
            Pseudo Genes (incomplete)         :: 88 of 184
            Pseudo Genes (internal stop)      :: 60 of 184
            Pseudo Genes (multiple problems)  :: 40 of 184
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-12 19:55:45
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 5337
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            FEEQ01000029.1.
            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
     source          1..5337
                     /collection_date="2006/2012"
                     /db_xref="taxon:1313"
                     /geo_loc_name="Netherlands"
                     /isolation_source="CSF"
                     /mol_type="genomic DNA"
                     /note="contig: ERS367508SCcontig000029"
                     /organism="Streptococcus pneumoniae"
                     /serovar="NA"
                     /strain="2842STDY5644069"
     region          1..5337
                     /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..5337
                     /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..5337
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[4552:4804](-)"
                     /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(4553..4804)
                     /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(<333..725)
                     /locus_tag="A1T31_RS11180"
                     /old_locus_tag="ERS367508_02184"
                     /pseudo=""
     CDS             complement(<333..725)
                     /GO_function="GO:0004055 - argininosuccinate synthase
                     activity [Evidence IEA]"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /GO_process="GO:0006526 - L-arginine biosynthetic process
                     [Evidence IEA]"
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002269502.1"
                     /locus_tag="A1T31_RS11180"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /old_locus_tag="ERS367508_02184"
                     /product="argininosuccinate synthase domain-containing
                     protein"
                     /pseudo=""
                     /transl_table=11
                     /translation="MSKEKVILAYSGGLDTSVAITWLKKDYDVVAVCMDVGEGKDLDFI
                     HDKALKVGAVESYVIDVKDEFATDYVLVALQSHAYYEQKYPLVSALSRPLISKKLVEIA
                     HQTGATTIAHGCTGKGNDQVEYQIAVA"
     gene            complement(742..1548)
                     /locus_tag="A1T31_RS11185"
                     /old_locus_tag="ERS367508_02185"
     CDS             complement(742..1548)
                     /codon_start=1
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1091: glutamine-binding lipoprotein glnH"
                     /gene_kind="biosynthetic-additional"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001038484.1"
                     /locus_tag="A1T31_RS11185"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS367508_02185"
                     /product="ABC transporter substrate-binding protein"
                     /protein_id="WP_061753378.1"
                     /transl_table=11
                     /translation="MNKMKKVLMTMFGLVMLPLLFACSNNQSAGIEAIKSKGKLVVALN
                     PDFAPFEYQKVVDGKNQIVGSDIELAKAIATELGVELELSPMSFDNVLASVQSGKADLA
                     ISGVSKTDELSKVFDFSTPYYTAKNKLIVKKSDLATYQSVNDLAQKKVGAQKGSIQETM
                     AKDLLQNSSLVSLPKNGNLITDLKSGQVDAVIFEEPVAKGFVENNPDLAIADLNFEKEQ
                     DDSYAVAMKKDSKELKEAVDKTIQKLKESGELDKLIEDAFKASIEK"
     misc_feature    1634..1648
                     /note="TFBS match to SypG, Regulator of biofilm formation
                     and host colonization, confidence: weak, score: 22.38"
                     /tool="antismash"
     gene            complement(1755..2396)
                     /locus_tag="A1T31_RS11190"
                     /old_locus_tag="ERS367508_02186"
     CDS             complement(1755..2396)
                     /codon_start=1
                     /gene_functions="transport (smcogs) SMCOG1000: ABC
                     transporter ATP-binding protein"
                     /gene_kind="transport"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000571330.1"
                     /locus_tag="A1T31_RS11190"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS367508_02186"
                     /product="ABC transporter ATP-binding protein"
                     /protein_id="WP_000571330.1"
                     /transl_table=11
                     /translation="MIELKNITKTIGGKVILDNLSLRIDQGDLVAIVGKSGSGKSTLLN
                     LLGLIDGDYSGRYEIFGQTNLAVNSAKSQTIIREHISYLFQNFALIDDETVEYNLMLAL
                     KYVKLPKKDKLKKVEEILERVGLSATLHQRVSELSGGEQQRIAVARAILKPSQLILADE
                     PTGSLDPENRDLVLKFLLEMNREGKTVIIVTHDAYVAQQCHRVIELGEGK"
     gene            complement(2393..4501)
                     /locus_tag="A1T31_RS11195"
                     /old_locus_tag="ERS367508_02187"
     CDS             complement(2393..4501)
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000723955.1"
                     /locus_tag="A1T31_RS11195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS367508_02187"
                     /product="bacteriocin-associated integral membrane family
                     protein"
                     /protein_id="WP_061753379.1"
                     /transl_table=11
                     /translation="MKKISNFCMLLLLLCTTFFVFNVNYTREVVRIQEMGKTVDSLDLY
                     LKDINEPAASVLRFFEDVSKEYKVSIIKTDSGDEVVKSGVFDKDTFPYQEFGISSLDFT
                     TDGEGVYSNKEISNKLGTIPTFLKAKPIQLMTFQTYIKDTSRSLNGRYTITSTQEMDKD
                     RIVQKWSDFFKIDQATLLEPTYKSAVEVINRDLLLSAIVFVLAILLLVLVTVYQPMMEM
                     KRVGVQKLLGFQDRAVLADVVKGNLYLLLGGALVINLGVFFLLDYKPKDLFPMLWLSHF
                     LLLQLYLFISWLTYLLIQKMTISSLLKGFSSFKFGLIFNYVMKIGTTILLTSLLIGVGR
                     SLEQENKELAYQQQWVSQGNYLTLETFKLNDNLWQEELAGSGKSTDYFYRFYQDLVEKT
                     QAGYVQSSSLPVKNFVQSEQIQQYQLTDTVDVYYANRNFLKSKGFKLPDTGIKKVILMP
                     ASTKGEEDKNQLLGKLIAFHSMKYEEQQKRTIEEMDVEIAYYEGDWSFFPYSDKRKENL
                     SNPIISLVNDSDMMWDEKASLSTTGLNNPIKIENTVQHQKEITELVEKLSDGNYLKFSS
                     IQAIQQEKVDSYRDAVRNFNLLFALFGLLSMMISYFLLVTTFLLKRRDIITKKFMGWKL
                     VDRYRPLLVLLLLGYSFPLLVLIFFAHAFLPLLLFAGFTCLDILFVLGLASRMEKRSLV
                     ELLKGGIL"
     gene            complement(4553..4804)
                     /locus_tag="A1T31_RS11200"
                     /old_locus_tag="ERS367508_02188"
     CDS             complement(4553..4804)
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters)
                     RiPP-like: Lactococcin_972"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001230165.1"
                     /locus_tag="A1T31_RS11200"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS367508_02188"
                     /product="lactococcin 972 family bacteriocin"
                     /protein_id="WP_000227120.1"
                     /sec_met_domain="Lactococcin_972 (E-value: 9.7e-34,
                     bitscore: 104.6, seeds: 6, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MVCSILASTSVLAVWVDGGQWNYGVGWSGNFGYSDYLHSTRSHTA
                     TVKDGNKFSKDRAEAEAWARASIFKFPPTGMEYFYGFE"
     misc_feature    5151..5164
                     /note="TFBS match to MogR, Repressor of flagellar motility
                     genes, confidence: strong, score: 25.42"
                     /tool="antismash"
     gene            <5250..>5337
                     /locus_tag="A1T31_RS12495"
                     /pseudo=""
     CDS             5250..>5337
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001268160.1"
                     /locus_tag="A1T31_RS12495"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /product="DNA-binding protein"
                     /pseudo=""
                     /transl_table=11
                     /translation="MILQRLEVYKNYQHLYDLRIAILLNLSTL"
ORIGIN
        1 aagcgaagga aagataaaaa agccgaggga tttcctcgac tctttacata ttatttgttc
       61 gttagttctt aataccagcc attgttaaac cagaagtttt tagctctgcc aagccacata
      121 gtgtgtttac tactatgtgg ccatgtcacc atgaatcgcc gaacgattta acgagaaagt
      181 atgactttta cgtttatccc aactcaatta tgacattttt ttcaaaagtc aatatatctc
      241 actttttcaa cgacaagaaa gaggctgcca attgaccaac ctcttattct gaacccatca
      301 ctccatcact ttttagcttc attcgctttc ttagcgactg caatctggta ttcgacttgg
      361 tcattcccct tacctgtaca accatgagca attgtagtcg ctcctgtctg atgcgctatt
      421 tcaaccaatt ttttagaaat aagagggcgg ctcaaggcag ataccaaggg gtacttttgt
      481 tcatagtagg catgtgactg gagagctact agcacataat ctgtagcaaa ttcgtcctta
      541 acatcaatga cataagattc gactgcccca accttaagag ccttatcatg gatgaaatct
      601 aagtctttcc cttcacccac atccatacaa actgcaacaa catcatagtc tttcttcagc
      661 caggtaatag caactgatgt gtctaaaccg ccagaatagg ccaaaattac tttttcttta
      721 ctcatgttct tttccttctt tctatttttc aatggacgct ttaaaggcat cctcaatgag
      781 tttgtctaat tccccagact ccttcaactt ttgaatggtt ttatcgactg cctctttcaa
      841 ttccttgcta tcttttttca tggctaccgc ataggaatca tcttgctctt tttcaaaatt
      901 gaggtctgcg attgctaaat caggattatt ttccacaaat cccttggcaa cgggttcttc
      961 aaaaataacg gcatccactt gccctgattt taaatctgtg attaaattcc catttttagg
     1021 cagagatacg agggaagaat tttgtagcaa atctttcgcc atcgtctctt gaatcgaacc
     1081 tttctgcgct ccgacctttt tctgcgccaa atcgttgaca gactgataag tggctaaatc
     1141 agattttttg acaatgagtt tattttttgc agtatagtag ggagttgaaa aatcaaacac
     1201 cttgctcagt tcatctgtct tagaaacacc tgatatggca aggtcagctt ttcctgattg
     1261 aacgctagcc agtacattgt caaaactcat aggagatagt tccaattcga cacctagttc
     1321 tgttgcgata gccttggcta attcgatatc tgaacccaca atctgatttt tcccatcaac
     1381 cactttttga tattcaaatg gagcaaaatc tggattgagg gctacaacca attttccttt
     1441 ggacttgatg gcttcaattc cagccgattg attgttacta caagcaaata gtagggggag
     1501 catcactaaa ccaaacatcg tcatcaacac cttcttcatc ttattcataa caaggcctca
     1561 tttatgttta ttctttttta ttgtataaat aatactccta tactcatcct ttgtcaagcc
     1621 taaattgaaa aaattttcaa tttgaaacaa aaaaaaccta gaaatactac ataaaatgtc
     1681 attcctaggc gtatttatgc tatttttctc tggaaaacat gagtattcag ccagtcaaaa
     1741 ggagctgaat gaactcattt tccctcgccc aattcaatga cacgatgaca ttgttgggct
     1801 acataagcat cgtgggtcac aataatgact gttttccctt ctcgattcat ctctaagaga
     1861 aacttcaaga ccaaatctct attttcagga tccagcgaac ctgtaggttc atcggctaaa
     1921 atcagctggc tgggttttaa gatggctcta gcaactgcaa ttcgttgttg ttcgccccca
     1981 gacaactcgg agaccctttg atgcaaagta gctgacaaac ctactctctc taaaatctct
     2041 tccacctttt tgagcttgtc tttcttaggc aatttcacat atttcagcgc cagcatgaga
     2101 ttgtactcga ccgtttcatc atcaatcagg gcaaaatttt gaaacagata agagatatgt
     2161 tcacggatta ttgtttgcga cttagcagaa ttaaccgcta gatttgtctg accaaaaatc
     2221 tcataccgtc cgctataatc accatctatc aaacccaata aatttaacaa ggtcgacttc
     2281 ccactaccac tcttaccaac aatagctacc aaatccccct gatcaatcct gagagataag
     2341 ttatccaaaa tcacttttcc cccaatggtt ttggtaatat ttttcaactc aatcataaga
     2401 tgcccccttt caataactct actagacttc ttttctccat cctagaagct aagcctagca
     2461 caaatagtat atccagacat gtaaaacctg caaacagtag aagtggtaag aacgcatggg
     2521 caaagaaaat caagactaga agagggaaac tatagcccag caagagcaga acgaggagag
     2581 gacggtagcg atcgaccagt ttccacccca taaacttctt ggtaatgata tccctgcgct
     2641 tcaataagaa agttgttact agtaagaagt aggaaatcat catgctaagg agaccaaaca
     2701 aagcaaagag taggttaaaa ttccgaacag catctctata agaatccact ttctcttgtt
     2761 gaatggcttg aatagatgaa aattttaaat aatttccatc tgacaatttc tcaactaact
     2821 ctgtaatctc tttttgatgt tgaaccgtat tttcaatttt aatcggatta tttaagccag
     2881 ttgttgacag ggaggctttc tcatcccaca tcatatcaga atcattgacc aagctaataa
     2941 ttggattgga gagattttcc tttcgcttat cactatatgg gaaaaatgac caatctcctt
     3001 cataataggc aatctcgaca tccatctcct ctatcgttcg tttttgctgc tcttcatact
     3061 tcatcgaatg aaaggcaatt aacttcccca agagctgatt tttatcttct tcacctttcg
     3121 tacttgctgg catcaaaata acttttttaa taccggtatc tggtagcttg aatcccttgc
     3181 tctttagaaa attgcgattg gcatagtaaa catccaccgt atctgttaac tgatattgct
     3241 gaatctgttc tgattggaca aaatttttta caggaagact gctactctgc acatagcccg
     3301 cctgcgtttt ttctaccaaa tcctgataaa atcgatagaa ataatctgta gatttccctg
     3361 accctgctag ctcttcttgc cacagattat cattgagttt gaaggtttct aaggtcaggt
     3421 aattaccttg acttacccac tgttgctgat aagcaagttc tttgttttct tgttctaaac
     3481 ttctgcccac cccaatcagt aaggacgtca gtaaaatagt tgtccctatt ttcatcacat
     3541 aattgaagat aagaccaaat ttgaaagatg aaaaaccttt cagcagagag ctgattgtca
     3601 ttttttggat taagaggtaa gtcaaccaac tgataaagag ataaagctgc aacagcaaaa
     3661 aatgagacaa ccacagcata ggaaacaaat cttttggctt ataatcaagc aagaaaaaca
     3721 cgcctagatt gatcacaaga gccccaccta ggaggaggta aaggttgcct tttacaacat
     3781 cagctaaaac agccctatct tgaaaaccaa gtaatttttg taccccaact cttttcatct
     3841 ccatcatcgg ttgatacact gtcactaaca caagaagcaa aatagccaag acaaaaacaa
     3901 tggcagataa aagcaaatct cgatttatga cttccactgc acttttgtag gtcggctcta
     3961 gcaaggtagc ctggtctatc ttgaaaaaat cgctccattt ctgtacaatc ctatccttgt
     4021 ccatctcttg tgtagaagtt atcgtatagc gaccatttaa actacgagat gtatccttga
     4081 tataggtttg aaaagtcata agctgaatag gtttggcttt tagaaaggtc ggaatcgtac
     4141 caagtttatt ggaaatttct ttattactat agactccttc accatctgtg gtaaaatcaa
     4201 gagaagaaat cccaaactct tggtagggga aggtatcttt atcaaaaaca ccagacttga
     4261 ccacctcatc accactgtct gttttgatga tggagacttt atactccttt gatacatcct
     4321 caaaaaatcg aagaacagac gctgcaggtt cgttaatatc tttcaaatac aaatccaaag
     4381 aatctacagt ctttcccatt tcttgaatcc gaaccacttc tcgtgtatag tttacattaa
     4441 aaacaaaaaa agtggtacac agaagcagga gtaacataca gaaattactg atttttttca
     4501 taaaagtgcc tccactacag ttttccctct ccaaatagga gagggaagaa ttttactcaa
     4561 atccatagaa atattccatt cccgttggtg ggaatttgaa gattgaagcc cgagcccatg
     4621 cctcagcttc tgcacgatcc ttagagaatt tatttccatc tttaacagtt gctgtatgag
     4681 agcgagtaga atgtaaataa tcagaataac caaaatttcc tgaccatcct actccatagt
     4741 tccattgacc accatcaacc catactgcca aaacacttgt agaagcaagt atactacata
     4801 ccattaaaga tgcaacacta attttctcat gatttatttc tcctattatc gagagctatt
     4861 ccgtagaaac agctatagta atttgtcaac aagtatcgta gtccattgga ctcaccttcc
     4921 ttctatctca tttcattttt aaacaacgaa cttactctta actaggagaa tagttctctt
     4981 ctgtatcagg tctttgaaca accagagtag tattaatcac actctaacta ttactcaaga
     5041 atcagcccaa taaacaatat ggatagcgct ttcaaatttt taaactctta tcccatcctt
     5101 ttatctatat aataagtgaa aatataataa ctgtcaagta atcgaagtga attttataaa
     5161 aaaaattaca agccaaattt gcaaagttta caataagccg ctagggcaat cgtctatcag
     5221 aatgtccgtt tatttgtcaa taatccgaga aaatcttgca acgcttagaa gtctataaaa
     5281 actatcaaca tttatatgac ttgcgaatag caatcctgct caacctttcc acactct
//
