PFAM acc# PFAM family # Logo Ambiguity Code Comments
PF00847 AP2-domain # 1 GGgAw.yGTGy AlignAce
PF00170 bZIP # 2 s.TGACGy AlignAce
PF00170 bZIP # 3 Tkr.GyMA AlignAce
PF00170 bZIP # 4 TGAsTCAs AlignAce
PF00170 bZIP # 5 caCGTGgc AlignAce
PF00170 bZIP # 6 TGCAAyms AlignAce
PF00170 bZIP # 7 mCACGTGk DimerFinder
PF00170 bZIP # 8 aTGACGTCAt DimerFinder
PF00170 bZIP # 9 aTGAsTCAt DimerFinder
PF00170 bZIP #10 aTTg..cAAt DimerFinder
PF00170 bZIP #11 gcCACGTGgc DimerFinder
PF00170 bZIP #12 gTGacGTG DimerFinder
PF00170 bZIP #13 TkACGTmA DimerFinder
PF03131 bZIP_Maf #14 GCtgaGTCA AlignAce (top ranked 28.8)
PF03131 bZIP_Maf #15 TGAsTCA DimerFinder
PF02045 CBFB_NFYA #16 CCAAysrg AlignAce (top ranked 32.9)
PF00859 CTF_NFI #17 tTGSC... AlignAce
PF00859 CTF_NFI #18 TGGc.....gCCA DimerFinder
PF02376 CUT #19 ..ATyGRT AlignAce
PF02376 CUT #20 CgATcG DimerFinder
PF02376 CUT #21 cgATCGAT DimerFinder
PF02319 E2F_TDP #22 GCGssAAa AlignAce
PF00178 Ets #23 smGGAagy AlignAce
PF00250 Fork_head #24 rYAAACAa AlignAce
PF00250 Fork_head #25 AryMAATA AlignAce
PF00250 Fork_head #26 AATATT DimerFinder
PF00250 Fork_head #27 kTTGTT DimerFinder
PF00250 Fork_head #28 TGTTTrTT DimerFinder
PF00250 Fork_head #29 TTTrTTTA DimerFinder
PF00320 GATA #30 .mGAyArG AlignAce
PF00320 GATA #31 yGATArs. AlignAce
PF02183 HALZ #32 AAT.ATTG AlignAce
PF02183 HALZ #33 cAAT.ATTg DimerFinder
PF00010 HLH #34 s.CrsGTG AlignAce
PF00010 HLH #35 CAgcTG DimerFinder
PF00010 HLH #36 cCACGTGg DimerFinder
PF00010 HLH #37 tCACGTGa DimerFinder
PF00505 HMG_box #38 AACAAwRr AlignAce
PF04814 HNF-1_N #39 g.yRAw.ATTAAC AlignAce
PF04814 HNF-1_N #40 GtTAAT.ATTAaC DimerFinder
PF00046 homeobox #41 TAAKKrss AlignAce
PF00046 homeobox #42 AAgyrcTT DimerFinder
PF00046 homeobox #43 AaT.AtT DimerFinder
PF00046 homeobox #44 TAATt.aATTA DimerFinder
PF00046 homeobox #45 TAATTAat DimerFinder
PF00447 HSF_DNA-bind #46 GAA..YTCkmG AlignAce
PF00447 HSF_DNA-bind #47 GAA..TTC DimerFinder
PF00447 HSF_DNA-bind #48 TTCtaGAA DimerFinder
PF00447 HSF_DNA-bind #49 TTCyaGAAg.TTC DimerFinder
PF00605 IRF #50 gAAA.yGAAAs AlignAce
PF00605 IRF #51 sTTTCrcTTT DimerFinder
PF00605 IRF #52 gTTTCrsTTTC DimerFinder
PF03165 MH1 #53 tGGCw... AlignAce
PF03165 MH1 #54 TGGc.....gCCA DimerFinder
PF00249 myb_DNA-binding #55 yAACsG.c AlignAce
PF00249 myb_DNA-binding #56 CATaCAT DimerFinder
PF00249 myb_DNA-binding #57 GGTwGGT DimerFinder
PF01056 Myc_N_term #58 CACGTGs.. AlignAce
PF01056 Myc_N_term #59 cCACGTGg DimerFinder
PF00292 PAX #60 raSCgKGrm AlignAce
PF00292 PAX #61 CGT.ACG DimerFinder
PF00292 PAX #62 TCA.gc.TGA DimerFinder
PF03792 PBX #63 tGATTGAT AlignAce
PF03792 PBX #64 TGATTGAT DimerFinder
PF00157 pou #65 ATGCAAAT AlignAce
PF00157 pou #66 ATGmATaw AlignAce
PF00157 pou #67 ATAAwTTAT DimerFinder
PF02257 RFX_DNA_binding #68 GTTGCcr.G..rm AlignAce (top ranked 38.0)
PF00554 RHD #69 GGrAa.yCCc AlignAce
PF00554 RHD #70 GGaawttCC DimerFinder
PF00554 RHD #71 GGawwtCC DimerFinder
PF00554 RHD #72 GGGGAwTCCCC DimerFinder
PF00853 Runt #73 yTGyGGT. AlignAce
PF00319 SRF-TF #74 CCwwAwaTrG AlignAce
PF00319 SRF-TF #75 CTATwwATAG DimerFinder
PF00319 SRF-TF #76 GGATCC DimerFinder (Artifact)
PF00319 SRF-TF #77 tCCwTwwAwGGa DimerFinder
PF02864 STAT_bind #78 TTCy.GGAA AlignAce
PF02864 STAT_bind #79 GyyTGTCTrrsGwsrkmGC AlignAce (Artifact)
PF02864 STAT_bind #80 gACAAGCTTGTc DimerFinder (Artifact)
PF02864 STAT_bind #81 GCGACGTCGC DimerFinder (Artifact)
PF02864 STAT_bind #82 GTCTGTCT DimerFinder (Artifact)
PF02864 STAT_bind #83 TGAGmkCTCA DimerFinder (Artifact)
PF02864 STAT_bind #84 TGAGsTswsAsCTCA DimerFinder (Artifact)
PF02864 STAT_bind #85 TGAGGTGAG DimerFinder (Artifact)
PF02864 STAT_bind #86 TTyC..GrAA DimerFinder
PF02864 STAT_bind #87 wTTCy.rGAAw DimerFinder
PF00352 TBP #88 G.ATATAwA AlignAce
PF00352 TBP #89 TATwTAT DimerFinder
PF01285 TEA #90 GGAATG.rr AlignAce
PF03299 TF_AP-2 #91 GsSwssgss AlignAce (top ranked 30.9)
PF03529 TF_Otx #92 kgrGaTTAgtg AlignAce (top ranked 24.9)
PF03106 WRKY #93 cgGtCamcg AlignAce
PF00105 zf-C4 #94 ..rGGTCA AlignAce
PF00105 zf-C4 #95 aGaACA...TGTtCt DimerFinder
PF00105 zf-C4 #96 AGGTCAc.gTGACCT DimerFinder
PF00105 zf-C4 #97 AGGTCATGACCT DimerFinder
PF00105 zf-C4 #98 tcAAGkTCAag DimerFinder
PF00105 zf-C4 #99 TGACCT...kTGACCT DimerFinder
PF00105 zf-C4 #100 TGACCTTTGACCyy DimerFinder
PF02701 zf-Dof #101 ...wAAAG. AlignAce
PF00172 Zn_clus #102 CGG..g.. AlignAce (top ranked 29.3)
PF00172 Zn_clus #103 CGGa..acwgt..tCCG DimerFinder


  • Artifact: This motif is not a valid Family Binding Profile. It derives from a fixed sequence flanking a region that was randomized in a selection experiment.
  • Top ranked: This motif is the top ranked motif produced by AlignACE for this family, but does not meet our significance threshold (Enrichment = 40).