Wed Aug 19 16:22:20 PDT 1998 This is a short peptide, so scores will be weak. wu-blast finds weak hit 1gcl[ABCD] -1.2378744 double-blast finds nothing The t84.t98_6 model finds 2cy3 -4.500 3cyr 1mbl[AB] -4.090 1btl [24]blm[AB] -4.050 1btl 1ldg -3.790 1ldg 1ayy[AC] -3.720 1apyA 1ty[uvwx] -3.550 1tyv 1tsp -3.540 1tyv 1php -3.430 1php 1pre[AB] -3.270 1preA The target98 library models find 1mnt[AB] -3.950 ? 1fgjA -3.670 1fgjA 1ft1A -3.630 1ft1A 1cfh -3.450 1cfh 1mykA -3.440 1mylA 1mylA -3.390 1mylA 1pgs_2 -3.130 1pgs 1vdfA -3.090 1lcf Summing both ways [24]blm[AB] -4.64 1btl 2cy3 -4.53 3cyr 1avc -4.3 1avc 1svq -4.16 1svr 1mbl[AB] -4.090 1btl 1ldg -4.08 1ldg 1svr -3.97 1svr 1zwe -3.96 1hph 1mnt[AB] -3.950 ? 1zwf -3.9 1zwf 1zwg -3.9 1zwg 256bA -3.9 256bA 1zwd -3.89 ? Using the fssp-viterbi library search: 1fgjA -6.500 1fgjA 1ft1A -5.710 1ft1A 2def -5.670 2def 1ife -4.620 1ife 1cfh -4.140 1cfh 1aszB -3.930 1aszB 1sesA -3.140 1sesA Using the target98-mixed library (with w0.5): 1fgjA -5.170 1fgjA 1gylA -3.880 1gox 2yhx -3.190 2yhx 1mylA -3.080 1mylA 1vin -3.010 1vin 1gox -2.770 1gox 1vcc -2.770 1vcc 1occE -2.350 1occE Using target98 viterbi search: 1pgs_2 -6.860 1pgs 1ft1A -6.760 1ft1A 1fgjA -6.310 1fgjA 1cfh -6.130 1cfh 1vin -5.570 1vin 1cpq -5.100 1cpq 2spcA -4.570 2spcA 1fbaA -4.490 1fbaA 2trcP -4.440 2trcP There is not a lot of consensus in the two directions! Looking at the most promising ones, the top non-self scores are 1ft1A/1ft1A-t84-vit.pw.dist:T0084 37 -7.93 -6.77 4blmA/t84-4blmA-vit.pw.dist:4blmA 256 -5.95 -6.45 1fgjA/1fgjA-t84-vit.pw.dist:T0084 37 -6.77 -6.31 1cfh/1cfh-t84-vit.pw.dist:T0084 37 -6.61 -6.13 1avc/t84-1avc-vit.pw.dist:1avc 642 -5.40 -5.96 1gox/1gox-t84-vit.pw.dist:T0084 37 -5.83 -5.31 2yhx/2yhx-t84-vit.pw.dist:T0084 37 -7.59 -4.98 1cpq/1cpq-t84-vit.pw.dist:T0084 37 -5.85 -4.63 2spcA/t84-2spcA-vit.pw.dist:2spcA 107 -3.66 -4.56 3cyr/t84-3cyr-vit.pw.dist:3cyr 107 -4.50 -4.47 1cfh/t84-1cfh-global.pw.dist:1cfh 47 -3.54 -4.16 1cfh/t84-1cfh-post.pw.dist:1cfh 47 -3.54 -4.16 1vin/1vin-t84-vit.pw.dist:T0084 37 -4.94 -3.90 1svq/t84-1svq-global.pw.dist:1svq 94 -4.11 -3.23 1svq/t84-1svq-post.pw.dist:1svq 94 -4.11 -3.23 1cpq/t84-1cpq-vit.pw.dist:1cpq 129 -3.31 -3.14 1avc/1avc-t84-vit.pw.dist:T0084 37 -4.82 -2.92 2def/2def-t84-vit.pw.dist:T0084 37 -3.18 -2.82 2yhx/t84-2yhx-global.pw.dist:2yhx 457 -5.31 -2.81 2yhx/t84-2yhx-post.pw.dist:2yhx 457 -5.31 -2.81 The 1ft1A-t84-vit alignment looks pretty good (a helix, a turn, and a helix): T0084 cgg...------REGVLKKLRAVENELHYNKSLLEE--------------...vkdelqkmrq R V R NEL Y LL E 1ft1A ...YHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFV... hhHHHHHHHTTLLTTHHHHHHHHHHHlttl Sliding the ends in doesn't improve things. The t84-4blmA-vit alignment gets a good match for the first helix: T0084 .....CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ...... GG E K LR 4blmA d108qIGGPESLKKELRKI-----------------------g134n. hTTLHHHHHHHHHHT tl Again, sliding in the end doesn't improve things. The 1fgjA-t84-vit alignment suggest that helix starting at ELH continues through LQK: T0084 ---ENELHYNKSLLEEVKDELQKM--- L Y K LEEV L M 1fgjA LKSDDPLYYKKGKLEEVENNLRSMGKL lltTSGGGHHHHHHHHHHHHHHHTtss Again, sliding in the end doesn't improve things. The t84-1avc-vit alignment is too short to be very useful, though it agrees with 4blmA on the location of the first helix: T0084 .....CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ...... K LR 1avc y346gDFNPDADAKALRK------------------------a283g. tTLLHHHHHHHHHH t Again, sliding in the end doesn't improve things. The 1gox-t84-vit alignment tries to suggest a single helix: T0084 -------------GGREGVLKKLRAVENELHY----- G GV K L E 1gox VFIGRPVVFSLAAEGEAGVKKVLQMMRDEFELTMALS eeelhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhh I think that the turn suggested by the 1ft1A alignment is more likely. The 2yhx-t84-vit alignment suggests a rather unlikely open configuration of the helices: T0084 cg...GREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ-- L V L 2yhx aaaxd-----XSLVEVHXXVFIVPPXILQAVVSILTTRXDDX llhhh HHHHHHHHHHHLLLHHHHHHHHHHHHHHHHhh The t84-3cyr-vit alignment is only 9 residues at the beginning of t83, and is not very convincing, since it is an extended loop on the surface of 3cyr. There doesn't seem to be much point in continuing on with the weaker alignments. STILL TO CHECK: 1cfh-t84-vit, 1cpq-t84-vit, t84-2spcA-vit Thu Aug 20 10:18:11 PDT 1998 T0084 c19lhYNKSLLEEVK-------------------------------------de8rq. YN LEE 1cfh .....YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVD...... LLLSSLSSLSsllll This is rather disordered at the beginning of the chain---I think I prefer the helix predicted for this region. T0084 c11klRAVENELHYNKSLLEEVKDELQKM----- L M 1cpq .....ADTKEVLEAREAYFKSLGGSMKAMTGVAK LLHHHHHHHHHHHHHHHHHHHHHHhhhhh Rather low residue conservation, but still a "mainly helical" vote. T0084 .....CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ...... G E KK 2spcA q34naGGNVEALIKK---------------------------h63gd. llLSLHHHHHHH hhh The turn at the beginning of a coiled-coil helix. What we have so far: CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ 1ft1A HHHHHHHTTLLTTHHHHHHHHHHH 4blmA TTLHHHHHHHHHHT 1fgjA TSGGGHHHHHHHHHHHHHHHT 1cfh LLLSSLSSLS 1avc TLLHHHHHHHHHH 1gox HHHHHHHHHHHHHHHHHHH 2yhx HHHHHHHHHHHLLLHHHHHHHHHHHHHHHH 1cpq LLHHHHHHHHHHHHHHHHHHHHHH 2spcA LSLHHHHHHH 3cyr BTTBLLLLL ------------------------------------- TLLHHHHHHHTTLLTTHHHHHHHHHHHHHHHHHHT consensus? Do we have to piece this one together? what a pain. If so it looks like 4blmA, followed by 1ft1A, followed by 1fgjA. Wed Sep 2 13:30:16 PDT 1998 Here are the comments for the submission: Since this peptide was supposed to be a de novo design, we did not expect evolutionary information from similar sequences in the protein data base, but we searched anyway. We found two proteins with pieces that matched the peptide: one from desmoplakin I [Homo sapiens] and one from ependymin [4 different species]. gi|2134996|pir||A38194 tvcldLDKVEAYRCGLKKIKNDLNLKKSLLATMKTELQKAQQihsqt. 607:643 E L N L KSLL K ELQK Q T0084 .....CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ...... 1:37 KKLR VENE H NK V gi|998296 diaegXFNYDSTAKKLRFVENESHANKTSHMDVLIHFEEGVLyeids. 20:56 gi|998286 diavgDFNYDSTAKKLRFVENESHANKTSHMDVLIHFEEGVLyemds. 31:67 gi|998304 diadgEFNYDSTAKKLRFVENESHSNKTSHMDVLIHFEEGVLyeids. 29:65 gi|998302 diaegEFNYDSTAKKLRFVENESHSNKTSHMDVLIHFEEGVLyeids. 27:63 Unfortunately, neither of these proteins have known structures, though the desmoplakin I match is to part of a 2-strand coiled-coil domain. We did not find a full-length match for this peptide in PDB, but we did find several partial matches. Based on these partial matches, we can piece together the prediction from three pieces 4blmA IGGPESLKKELRKI 4blmA LLLHHHHHHHHHHL GG E K LR 1ft1A RQWVIQEFRLWDNELQYVDQLLKE 1ft1A HHHHHHHLLLLLLHHHHHHHHHHH R V R NEL Y LL E 1fgjA DDPLYYKKGKLEEVENNLRSM 1fgjA LLGGGHHHHHHHHHHHHHHHL L Y K LEEV L M and predict the following secondary structure: CGGREGVLKKLRAVENELHYNKSLLEEVKDELQKMRQ LLLHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHLLL