LOCUS       NZ_CPTT01000042         5491 bp    DNA     linear   CON 13-DEC-2024
DEFINITION  Streptococcus pneumoniae strain 10F/2, whole genome shotgun
            sequence.
ACCESSION   NZ_CPTT01000042
VERSION     NZ_CPTT01000042.1
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 (10-MAR-2015) SC, Wellcome Trust Sanger Institute, CB10
            1SA, United Kingdom
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001138385.1-RS_2024_12_13
            Annotation Date                   :: 12/13/2024 01:30:31
            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)                     :: 2,083
            CDSs (total)                      :: 2,048
            Genes (coding)                    :: 1,909
            CDSs (with protein)               :: 1,909
            Genes (RNA)                       :: 35
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 29
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 60 of 139
            Pseudo Genes (incomplete)         :: 78 of 139
            Pseudo Genes (internal stop)      :: 32 of 139
            Pseudo Genes (multiple problems)  :: 26 of 139
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 11:01:49
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 5491
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CPTT01000042.1.
            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..5491
                     /collection_date="1956"
                     /db_xref="taxon:1313"
                     /geo_loc_name="USA"
                     /host="Homo sapiens"
                     /isolation_source="not known"
                     /mol_type="genomic DNA"
                     /organism="Streptococcus pneumoniae"
                     /serovar="10F"
                     /strain="10F/2"
     region          1..5491
                     /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..5491
                     /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..5491
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[506:2726](+)"
                     /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      507..2726
                     /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            507..2726
                     /locus_tag="AEH42_RS10195"
                     /old_locus_tag="ERS011481_01979"
     CDS             507..2726
                     /GO_component="GO:0055052 - ATP-binding cassette (ABC)
                     transporter complex, substrate-binding subunit-containing
                     [Evidence IEA]"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /GO_function="GO:0008233 - peptidase activity [Evidence
                     IEA]"
                     /GO_function="GO:0016887 - ATP hydrolysis activity
                     [Evidence IEA]"
                     /GO_function="GO:0042626 - ATPase-coupled transmembrane
                     transporter activity [Evidence IEA]"
                     /GO_function="GO:0140359 - ABC-type transporter activity
                     [Evidence IEA]"
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters)
                     RiPP-like: TIGR01193"
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) Peptidase_C39"
                     /gene_functions="transport (smcogs) SMCOG1288: ABC
                     transporter related protein"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001856353.1"
                     /locus_tag="AEH42_RS10195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS011481_01979"
                     /product="peptidase domain-containing ABC transporter"
                     /protein_id="WP_050119720.1"
                     /sec_met_domain="Peptidase_C39 (E-value: 2e-33, bitscore:
                     103.7, seeds: 36, tool: rule-based-clusters)"
                     /sec_met_domain="TIGR01193 (E-value: 1.3e-171, bitscore:
                     561.1, seeds: 5, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MLKKYPCTMQHDQSDCAAAVVSTVLLSYKKELSIMKIREIIGTDM
                     YGTTVSGIVSGLNKLNFTVKAVRVALEDLTPKLTFPAILQVKNDLGQNHFVVLHSIKRN
                     SKFYVADPASGIRKMSSDELGEIYQGITLFMVPNSDFERGKLKGKGLLDLFGRLIFNQK
                     GLISTVILASFVLSIIGILSSLFSKVIMDEVIPYALKNSLYMFLIVFGIVSFLQTLLSA
                     FRQHVLLFLSRKIDIPVLMGYYDHIIHLPYSFFGSRRVGDVLTRFQDAMTIKNVFTSVS
                     ISLVMDITLSVISAVVLWTINQSLFLILVFMVIVNIILIYCFKKPYKKINHEQMEANGL
                     LNSQLIESIRNIDTIKSQHDEEQRLNKIEEKFVHTLEIGYKEGVLQNIQSTISSMTSTM
                     GGLLFMGVGALFIIDGKMTIGDLLVFQTLSQYFTEPIQNLVGLQLTFQEVQVAVSRLQE
                     LMEVDREDIALDYSIRDFTLCDDIEFKDVTFAYGSRPPVIKNFNLRIKQGEKIAFVGES
                     GAGKSTIVRLLLRFINPNEGKICIGANDLSDLDYGKLRKKISYIPQTIELFTGTIIDNL
                     KIGNPSVTYEDMVRVCRIVGIHDTIQRLQNRYGSFVEEGGQNFSGGEKQRLAIARALLS
                     KADLYIFDEATSNLDSFSEQIIQDLIFNKIMDKTTIVVAHRLSTILRCDKICFLENGTI
                     VEYGTHEELMAKNGKYARMVGLQSVQVNQQIQSQAVLDTEEVTYG"
     gene            2719..3186
                     /locus_tag="AEH42_RS10200"
                     /old_locus_tag="ERS011481_01980"
     CDS             2719..3186
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001096140.1"
                     /locus_tag="AEH42_RS10200"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS011481_01980"
                     /product="hypothetical protein"
                     /protein_id="WP_001096141.1"
                     /transl_table=11
                     /translation="MAKLEVKDNKKLVLKSVICKKLHDTKVEDVDQEINKFHQHLQLLK
                     AQIFGPLIVKSCGTTIHDDGLITTDFEFYIQAHNAQQYSNIYDVQDSISVPYCLYVRFE
                     DSPEYLQYAYSKLDLYVYENDIQTDGIVYTVYVNSSPEKMVVDIFRPIVSL"
     gene            3183..4535
                     /locus_tag="AEH42_RS10205"
                     /old_locus_tag="ERS011481_01981"
     CDS             3183..4535
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001865356.1"
                     /locus_tag="AEH42_RS10205"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS011481_01981"
                     /product="HlyD family efflux transporter periplasmic
                     adaptor subunit"
                     /protein_id="WP_050119722.1"
                     /transl_table=11
                     /translation="MKLYNKSELRYSRIFFDKRPPAFAFILIISTAIILSGALVGAAYI
                     PKNYIVKANGNSVITGTEFLSAIGSGKVVTLHKSEGDMVNAGDVIISLSSGQEGLQASS
                     LNKQLEKLRAKEAIFQKFEQSLNEKYNHLSNSGEEQEYYGKVEYYLSQLNSENYNNGTQ
                     YSKIQDEYTKLNKITAERNQLDDDLQALQNELLQLQQQGDSPSLSDTTSADNKAKLETK
                     ISEITTKIEALKTNITSKNSEIDSQQSNIKDMNRTYNNPTSQAYNIYAQLISELGTARS
                     NNNKSITELEANLGVATGQDKAHSILAPNEGTLHYLVPLKQGMSIQQGQTIAEVSGKEK
                     GYYVEAFVLASDISRVSKGAKADVAITGVNSQKYGTLKGQVRQIDSGTISQETKEGNIS
                     LYKVMIELETLTLKHGSETVVLQKDMPVEVRIVYDKETYLDWILEMLSFKQ"
     gene            4681..5061
                     /locus_tag="AEH42_RS10210"
                     /old_locus_tag="ERS011481_01982"
     CDS             4681..5061
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000424421.1"
                     /locus_tag="AEH42_RS10210"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="ERS011481_01982"
                     /product="SP_0115 family bacteriocin-like peptide"
                     /protein_id="WP_000424421.1"
                     /transl_table=11
                     /translation="MELVLPNNYVALEQEEMMYLDGGGVGRNWWNSRGSFATVLDVDLA
                     IYSGGATIYSAYAIKKAISANRGAITRTLRSLIIKHVGSAAGHLVNTALNVALTVTGFS
                     LGGAIAYGADWADGSLDGYIFA"
     gene            5063..5269
                     /locus_tag="AEH42_RS12270"
     CDS             5063..5269
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014632394.1"
                     /locus_tag="AEH42_RS12270"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="hypothetical protein"
                     /protein_id="WP_014632394.1"
                     /transl_table=11
                     /translation="MKHFFAGIGEINFVSYLLYICVGIAPFFHVYIIGSEMNFVKIVLS
                     ILGIIFVCILTIARIYRTFFYKE"
     gene            complement(5288..>5491)
                     /locus_tag="AEH42_RS11935"
     CDS             complement(5288..>5491)
                     /codon_start=1
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /locus_tag="AEH42_RS11935"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /product="hypothetical protein"
                     /protein_id="WP_222851848.1"
                     /transl_table=11
                     /translation="RDLLPSEGKIKKPRELLDLFIESPNDLTRKYDFYVYPNSIMTFFS
                     KVNISHFFNDKKEADNLPTSCF"
ORIGIN
        1 tcacgtattt ctttatagac ctttccgaaa tcataacgca tgattttctc cttttcgtga
       61 aaaaagttaa caaacaataa aattttgtta aaaatattgt atcatagcaa tgtaaaaagt
      121 aaaaaagaaa gtcgaaataa atttgtgaaa aaagttaacg taattttaaa atgagcttaa
      181 taagaggtac tatgtaggta gaaaataaag ataggagaaa aagtatgaat aaaaaaatat
      241 tttgtattct agtatgtatt atattattga ttagtctggc tataatcttt ccatggggct
      301 ggccgatata atgtaaggga gtttgagttg ttaaaggagg ctcagtcctt gggcaaaaat
      361 ctgctgtact acaatgcttg gaaagatatc aagaacaaag aatgatacgg ttgaaaataa
      421 attaattcaa gaactactgg gcagtgattg aggtttgggt gacatcaaag aaaagttaga
      481 ttaattctaa agaattgagt atttctatgt taaaaaaata tccttgtacg atgcaacatg
      541 accagtcaga ttgtgctgcg gcagttgttt caacagttct tttatcttac aaaaaggaac
      601 tatcaatcat gaagattagg gaaattattg gtacagacat gtatggaacg actgtcagtg
      661 gtattgtttc aggtctgaat aagttgaatt ttacagtaaa agctgttcga gtagcactgg
      721 aagatttgac tccaaaatta acatttcctg cgattcttca agttaagaat gatttaggtc
      781 aaaatcattt tgtggtatta catagtatca aaaggaatag taagttctac gtagcagacc
      841 ctgctagtgg catacgcaag atgtcaagtg acgaactggg agaaatttat caaggtatta
      901 ctctttttat ggttccaaat tcggattttg aaagagggaa actaaaggga aaaggacttc
      961 ttgatttatt tggaaggtta atttttaatc aaaaaggatt gattagtaca gtcatattag
     1021 cttcctttgt tttaagtatc attggtattt tatcgagtct cttttcaaaa gttatcatgg
     1081 acgaggtgat tccatatgct ttaaaaaata gtctgtatat gtttttgata gtatttggaa
     1141 tagtgtcgtt cttacagact cttctatctg catttcgtca gcacgttctt ttgtttctat
     1201 ctcgaaaaat tgatataccg gttttaatgg gatattatga ccatattatt catcttcctt
     1261 atagtttttt tggaagtcgt agagttggtg atgttttaac gagatttcaa gatgcgatga
     1321 cgataaagaa tgtgtttacg tcagtctcta tttcattagt catggatatc accttgtcag
     1381 ttattagtgc ggttgtcctt tggactatta atcaatcttt atttctgata ttagttttta
     1441 tggttattgt taacatcatt cttatatact gttttaaaaa gccttataaa aaaattaatc
     1501 atgaacaaat ggaagcaaat ggacttctta attcacagtt aattgaatct attcgtaaca
     1561 ttgataccat taagtctcag catgacgagg aacaacgttt aaacaaaatt gaagaaaaat
     1621 ttgttcatac tttagaaatt ggttataaag agggtgtttt gcagaatatt caatctacaa
     1681 tatcttcaat gacctcaacc atgggtgggt tattatttat gggagtgggc gccttattta
     1741 tcattgatgg aaaaatgact attggggacc tcttggtttt tcagacatta agtcaatatt
     1801 ttacagaacc tattcagaat ttagttggtt tgcagttaac ctttcaagag gtacaggttg
     1861 cggttagtcg acttcaagaa ttgatggaag tagatcgtga agacattgcc ttggattata
     1921 gtattagaga cttcacctta tgtgatgata tcgagtttaa agatgtaaca tttgcctatg
     1981 gttcgcgccc acctgttatc aagaacttta atttgcgaat taaacaagga gaaaaaatag
     2041 cttttgttgg tgaaagtgga gcaggaaaaa gtacgatagt tcgtttatta ttaagattta
     2101 taaatccgaa tgaggggaaa atttgtatag gagcaaatga cttatcagat cttgactatg
     2161 gtaaactacg taagaaaatt tcctacattc cacagaccat agaactcttt acagggacaa
     2221 ttattgataa tctaaaaatt ggtaatcctt ctgttacata tgaggatatg gtgagagttt
     2281 gtcgtattgt tggtattcat gatacgattc aacgccttca aaatcgttat ggctcctttg
     2341 tagaagaagg cggtcaaaat ttctcgggtg gagagaaaca acgattggct attgcaagag
     2401 cactactgag taaagctgat ttgtatatat ttgatgaggc aacctctaac ttagattcat
     2461 ttagtgaaca gattattcag gatttaatct ttaataaaat aatggataag acaacaattg
     2521 tagtagccca caggctgtct acaattcttc gatgtgataa gatatgcttt ttagaaaatg
     2581 ggactattgt ggaatatggg actcatgaag aactaatggc gaaaaatgga aagtatgcta
     2641 gaatggttgg tttgcagagc gttcaagtga atcaacaaat tcagtcacag gctgtgttag
     2701 atacagagga ggttacttat ggctaagtta gaggtaaaag ataataaaaa actggtacta
     2761 aagtcagtta tctgtaaaaa gttacatgat acaaaagtag aagatgtaga tcaggaaatt
     2821 aataaatttc atcaacattt gcagttgtta aaagcacaaa tttttggtcc attaattgta
     2881 aaaagttgtg gtactactat tcatgatgat ggattaataa cgactgattt tgagttttat
     2941 attcaagctc ataatgctca acagtacagt aacatttatg atgtacagga ttctatctct
     3001 gttccatatt gtttatatgt tcgttttgaa gacagtccag agtatctaca gtatgcgtat
     3061 tctaaattgg atctatatgt ctatgaaaat gatattcaaa cggatgggat tgtctataca
     3121 gtttatgtta attcttctcc tgaaaaaatg gtagtagata tttttagacc aattgtaagc
     3181 ctatgaaatt atataataaa tcagaattac gttattctcg tattttcttt gataagagac
     3241 caccagcttt tgcgtttatt ctcattattt caactgctat tatcttaagc ggtgcattgg
     3301 ttggcgcagc ttatataccc aaaaactata ttgtaaaagc gaatggaaat tcagttataa
     3361 caggtacaga gttcctatca gcaattggtt cagggaaggt agttacttta cataagtcag
     3421 aaggagatat ggtaaatgct ggagatgtca ttatttcgtt atcaagtgga caagaaggtt
     3481 tacaagcgag ctctttaaat aaacaattgg agaagttacg tgcaaaagaa gctatctttc
     3541 aaaaatttga acaatcatta aatgagaaat acaatcattt atctaattct ggtgaagaac
     3601 aggaatatta tgggaaagtt gaatactatc tgtctcagtt aaactcggaa aattataata
     3661 atggtaccca gtattcaaag attcaggatg aatatacgaa gttgaataaa ataacagctg
     3721 aaagaaatca gttagatgac gacttgcaag ctctacaaaa tgaattgctt caacttcaac
     3781 agcaaggaga ctcgccttct ctatcagata cgacatcagc tgataacaaa gctaagttag
     3841 aaactaagat atcagaaata acaacaaaaa tcgaagcatt aaaaacaaat attacttcta
     3901 agaatagcga gattgatagt caacaaagca atattaagga tatgaaccgt acctataata
     3961 atccaacttc tcaggcttat aatatttatg ctcaattaat tagtgagtta ggtactgctc
     4021 gttcaaacaa caataaaagt attacagagc ttgaggctaa tcttggagtg gcaacaggtc
     4081 aagataaagc acatagtata ttagcgccaa atgaaggtac tctgcattat ctggtacctt
     4141 tgaaacaagg aatgtctatt cagcaggggc aaacgatagc agaagtttca gggaaagaaa
     4201 aaggttacta tgtagaagct tttgtacttg cgagtgatat ttctcgtgtt tcgaaaggag
     4261 caaaagctga tgttgctatt actggtgtaa atagtcaaaa atatggaaca ctaaagggac
     4321 aagtcagaca gattgattca ggaacaattt cccaagaaac gaaagaaggc aatattagtc
     4381 tttataaagt catgatagaa ttagaaacct taactctaaa acatggaagt gagacagtcg
     4441 tcctccaaaa ggatatgcca gttgaagtgc ggattgtcta tgataaagaa acctatcttg
     4501 attggatttt ggaaatgtta agtttcaagc aataattggt tttaaacatt aagtcaccta
     4561 taaaataaag taagataaag gaaagatatc ttatctaggt aactaagtgc tataaacaaa
     4621 gtcaacgatc acttgttagg aaactatcct aaccatgctt aataaaaaag gagaatttta
     4681 atggaactcg tattaccaaa taattatgtt gctcttgagc aagaagagat gatgtatctt
     4741 gatgggggtg gtgttggtcg taactggtgg aatagtagag gtagttttgc aacagttctg
     4801 gatgtagatt tggccatcta tagtggtggt gcaacaattt attctgctta tgcgataaaa
     4861 aaagctatct cagctaatag aggggctatt acgagaacat tacgtagttt aataattaaa
     4921 catgtaggta gtgcagctgg ccatttagtc aatactgcac taaacgttgc actaactgtt
     4981 actggatttt cactaggtgg agcaatcgca tatggggctg attgggctga cggtagctta
     5041 gatggttata tttttgctta aaatgaaaca tttttttgca ggaattggtg aaataaactt
     5101 tgtaagttat ttattgtata tatgtgtagg aatagcccct ttttttcacg tatatataat
     5161 aggttctgaa atgaattttg tgaaaatagt gttatctatt ttgggaatta tatttgtttg
     5221 tattttaact attgctcgaa tttataggac ttttttctat aaagaatagt ttggacttga
     5281 aatgtattta aaaacaagag gttggtagat tatcagcctc tttcttgtcg ttgaaaaagt
     5341 gagatatatt gacttttgaa aaaaatgtca taattgagtt gggataaacg taaaagtcat
     5401 actttctcgt taaatcgttc ggcgattcta tgaaaaggtc gaggagctcc ctcggctttt
     5461 ttatctttcc ttcgcttggt aatagatctc t
//
