CyanoPatt

Search a Pattern against Cyanobacterial genomic regions

Search Portal Pattern Dataset     P-con Model: Acaryochloris_marina_MBIC11017 Anabaena_90 Anabaena_cylindrica_PCC_7122 Anabaena_variabilis_ATCC_29413 Arthrospira_platensis_NIES_39 Calothrix_PCC_63039 Calothrix_PCC_7507 Chamaesiphon_PCC_6605 Chroococcidiopsis_thermalis_PCC_7203 Crinalium_epipsammum_PCC_9333 Cyanobacterium_PCC_10605 Cyanobacterium_stanieri_PCC_7202 Cyanobium_gracile_PCC_6307 Cyanothece_ATCC_51142 Cyanothece_PCC_7424 Cyanothece_PCC_7425 Cyanothece_PCC_7822 Cyanothece_PCC_8801 Cyanothece_PCC_8802 Cylindrospermum_stagnale_PCC_7417 Dactylococcopsis_salina_PCC_8305 Geitlerinema_PCC_7407 Gloeobacter_JS Gloeobacter_violaceus_PCC_7421 Gloeocapsa_PCC_7428 Halothece_PCC_7418 Leptolyngbya_PCC_7376 Microcoleus_PCC_7113 Microcystis_aeruginosa_NIES_843 Nostoc_azollae__0708 Nostoc_PCC_7107 Nostoc_PCC_7120 Nostoc_PCC_7524 Nostoc_punctiforme_PCC_73102 Oscillatoria_acuminata_PCC_6304 Oscillatoria_PCC_7112 Pleurocapsa_PCC_7327 Prochlorococcus_marinus_AS9601 Prochlorococcus_marinus_CCMP1375 Prochlorococcus_marinus_MIT_9211 Prochlorococcus_marinus_MIT_9215 Prochlorococcus_marinus_MIT_9301 Prochlorococcus_marinus_MIT_9303 Prochlorococcus_marinus_MIT_9312 Prochlorococcus_marinus_MIT_9313 Prochlorococcus_marinus_MIT_9515 Prochlorococcus_marinus_NATL1A Prochlorococcus_marinus_NATL2A Prochlorococcus_marinus_pastoris_CCMP1986 Pseudanabaena_PCC_7367 Rivularia_PCC_7116 Stanieria_cyanosphaera_PCC_7437 Synechococcus_CC9311 Synechococcus_CC9605 Synechococcus_CC9902 Synechococcus_elongatus_PCC_6301 Synechococcus_elongatus_PCC_7942 Synechococcus_JA_2_3B_a_2_13 Synechococcus_JA_3_3Ab Synechococcus_PCC_6312 Synechococcus_PCC_7002 Synechococcus_PCC_7502 Synechococcus_RCC307 Synechococcus_WH_7803 Synechococcus_WH_8102 Synechocystis_PCC_6803 Synechocystis_PCC_6803_substr__GT_I Synechocystis_PCC_6803_substr__PCC_N Synechocystis_PCC_6803_substr__PCC_P Thermosynechococcus_elongatus_BP_1 Thermosynechococcus_NK55 Trichodesmium_erythraeum_IMS101 all organism 0 1 2 Mismatches Insertions Deletions Substitutions Type: Nuleotide Protein Database: Upstream sequence from -500 to +50 unspliced ORF Upstream sequence with no gene overlap Protein Stress Element Organism Cis element Regulated gene Binding factor Function Reference Heat CIRCA Bacillus subtilis TTAGCACTCN{9}GAGTGCTAA dnaK and groESL operons HrcA negative regulation on Heat shock 8113175 Light, Heat CIRCA Synechocystis PCC6803 TTAGCACTCN{9}GAGTGCTAA groE HrcA Light and heat response 17434494 Light, Heat K-box Synechocystis PCC6803 GTTCGGNNANCCNNAC groE HrcA Light and heat response 17434494 Light, Heat N-box Synechocystis PCC6803 GATCTA groE HrcA Light and heat response 17434494 light HLR1 Synechocystis PCC6803 [GT]TTACA[TA][TA] hliB RpaB 17294172 light Synechocystis PCC6803 RWWTRGGYNNYY pedR 17035238 light HLR1 Synechocystis PCC6803 AAAACAATtcTTTACATA PsaE RpaB 19074384 co Synechocystis PCC6803 AAACCTTGACATTN{5}AATGTTAAGGTTT corT corR 10692354 heat inverted repeat (IR) Thermosynechococcus elongatus ACAAgcAAATTTagTTGT hspA 12270139 ox inverted repeat sequence Synechocystis PCC6803 ATAATTAT PerR 15150218 ox perR box Synechocystis PCC6803 ATAATTATTCTATCTAATA PerR 15150218 ox perR box Synechocystis PCC6803 ATAATTATTCTATCTAATA ahpC PerR 15150218 co2 Synechocystis PCC6803 ATCN{9}GAT slr0040, slr0041, slr0043, and slr0044 CbbR 11222586 light Synechocystis PCC6803 CAACN{6}GTTG SufR 17827500 fe Pseudomonas aeruginosa CGAGGAA and CGTGGAT, 8626326 Synechocystis PCC6803 CTAN{9}CTA lexA LexA-related protein 18555801 Synechocystis PCC6803 CTAN{9}CTA crhR LexA-related protein 18555801 green light Nostoc punctiforme ATCC 29133 CTTTNCNATTTCTTTNCNATTT CcaR 20404166 n-box GATCTA groESL1 17434494 light HLR1 Synechocystis PCC6803 GTAACAATaaTTAAAAAT PsaAB RpaB 19074384 nitrogen Synechocystis PCC6803-coccus GTAN{8}TAC nir NtcA- 8026471 nitrogen Synechocystis PCC6803 GTAN{8}TAC sll1423 NtcA- 11161053 light HLR1 Synechocystis PCC6803 GTTACAGTtcTTGACAAA PsaD RpaB 19074384 light HLR1 Synechocystis PCC6803 GTTACGATtaTTTACAAT PsaFJ RpaB 19074384 k-box GTTCGGNNANCCNNAC groESL1 17434494 heat/light K-box and N-box Synechocystis PCC6803 GTTCGGNNANCCNNAC and GATCTA HrcA 17434494 light HLR1 Synechocystis PCC6803 GTTGCAATacTTAACAAA PsaK RpaB 19074384 circadian timing Synechococcus elongatus PCC 7942 LxxxExxxL, LR, and TxxGxGY kaiA, kaiB, and kaiC RpaA 16882723 phosphate Synechocystis PCC6803 PyTTAAPyPy[TA] phoA, sphX, and pstS SphR 14707128 - Anabaena RGTACNNNDGTWCB LexA 17630298 light Synechocystis PCC6803 RWWTRGGYNNYY hlL PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY chlN PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY chlB PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY slr1957 PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY ndhD2 PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY rpe PedR 17035238 light Synechocystis PCC6803 RWWTRGGYNNYY PedR 17035238 bacillus RWWTRGGYNNYY sigK GerE 11418558 Anabaena sp. PCC 7120 TATGAAAAGAATATGAGAA mntH ManR 12417709, 15063797 ,15604770,15742142 ox Synechocystis PCC6803 TCAATGN{10}ATCAAT Sll1594 Sll1594 11136465 ox Synechocystis PCC6803 TCAATGN{10}ATCAAT slr1727 Sll1594 11136465 lignt, salt Synechocystis PCC6803 TCAATGN{10}ATCAAT Sll1594 11136465 osmotic Synechocystis PCC6803 TCAATGN{10}ATCAAT sll1594, slr1727 11136465 arsenic Synechocystis PCC6803 TCATN{7}TTTG ArsR 12949088 light Synechocystis PCC6803 TGTGAN{6}TCACA Crp 12085767 light Synechocystis PCC6803 TGTGAN{6}TCACA slr1667 Crp 12085767 ox Synechocystis PCC6803 TGTTCCTCCTAACATCGG sll1621 Type 2 peroxiredoxins like 15047877 ox Synechocystis PCC6803 AGTCTATCTAGCTTAACA sll1621 Type 2 peroxiredoxins like 15047877 nitrogen Synechocystis PCC6803 TN{11}A NtcB 11566981 h2o2 Synechocystis PCC6803 TTN{5}AAC abrB2 22865847 heat CIRCE Synechocystis PCC6803 TTAGCACTCN{9}GAGTGCTAA groESL1 17434494 light, low CO2 conditions CbbR binding motif Synechocystis PCC6803 TTAN{7}TAA psbAII CmpR 15101988 light, low CO2 conditions CbbR binding motif Synechocystis PCC6803 TTAN{8}TAA psbAIIi CmpR 15101988 light HLR1 Synechocystis PCC6803 TTCAAATTctGTTACATC PsaC RpaB 19074384 light L Box F. diplosiphon TTGCACAN{4}TTGCACA RcaC 18346116 via 20833804 light L box Fremyella diplosiphon TTGCACANNNNTTGCACA RcaC 20833804 nitrogen Synechococcus sp. PCC 7942 ttGTAaacaatcacTACa (or) tGTAgcacccgtagCa nblA NblR 11532155 light HLR1 Synechocystis PCC6803 TTTAAAAAaaTTCATTAA PsaL RpaB 19074384 Search Result Stats Raw Output Organism Database : Number of sequences matched : Query time : Add your pattern and click search pattern button! Search Type Character Meaning Examples Peptide Searches IFVLWMAGCYP TSHEDQNKR Exact match DQGT J Any hydrophobic residue (IFVLWMAGCY) AAAAAAJJ O Any hydrophilic residue (TSHEDQNKR) TTTTTTOO B D or N FLGB Z E or Q GLFGZ X or . Any amino acid DXXXNW..VSK Nucleotide searches ACTGU Exact match ACCGGCGTAA R Any purine base (AG) AAGGCCGGRRRR Y Any pyrimidine base (CT) CCCATAYYGGYY S G or C YGGTWCAMWTGTY W A or T M A or C K G or T V A or C or G CCGG...WHW.{3,5}HWH...CCGG H A or C or T D A or G or T B C or G or T N or X or . Any base ATGCTNNNNATCG All searches: [ ] A subset of elements [TC] = T or C [WFY]XXXDN[RK][ST] [^ ] An excluded subset of elements [^TA] = not T or A, (matches nucleotides C or G) NDBB...[VILM]Z[DE]...[^PG] ( ) Specifies a sub-pattern (YPT) = YPT (YDXXX){2,} {m,n} {m} = exactly m times {m,} = at least m times {,m} = 0 to m times {m,n} = between m and n times L{3,5}X{5}DGZ < Constrains pattern to N-terminus or 5' end <MNTD (pep) <ATGX{6,10}RTTRTT (nuc) > Constrains pattern to C-terminus or 3' end sbgz> (pep) yattrtga> (nuc)

Bioinformatics Lab | National Facility for Marine Cyanobacteria