Kevin Karplus 10 May 1998 The claimed homology seems to be to 3pte with more distant homology to 2bltA The 3pte fssp file has identical sequences 1ceg and 1cef, and high Z scores for 2bltA, 1btl, and 1pmd. The target model gets several high scores (better than -100), with no other significant scores: 1blsA, 1blsB, 2bltA, 2bltB, 1cef, 1ceg, 3pte, and 2pteE. The template models score only 3pte and 2bltA well, and they both score excellently. Summing in both directions gives 8 siginificant scores: t49 2bltA -384.9 t49 1blsA -294.470 => 2bltA t49 1blsB -294.470 => 2bltA t49 2bltB -294.470 => 2bltA t49 3pte -220.27 t49 1cef -119.440 => 3pte t49 1ceg -119.440 => 3pte t49 2pteE -117.190 ? obsolete for 3pte? I think we want fssp and constrained fssp alignments for 2bltA and 3pte, in order to get good alignments. From karplus@cse.ucsc.edu Mon May 11 01:15:57 1998 Return-Path: karplus@cse.ucsc.edu Date: Mon, 11 May 1998 01:15:56 -0700 From: Kevin Karplus To: markd@cse.ucsc.edu Cc: karplus@cse.ucsc.edu Subject: still more alignments to create 2bltA and 3pte for target t49. -------------------------------------------------- 11 May 1998 Kevin Karplus 3pte-t49-const-global alignment looks pretty good. Still waiting for other alignments to be done. -------------------------------------------------- Kevin Karplus 26 May 1998 Currently I favor t49-3pte-global or t49-2bltA-global -------------------------------------------------- Kevin Karplus Wed Jul 15 17:35:12 PDT 1998 I redid the Makefile and ran to get blast and double-blast results. Top blast hit is 1cef, 1ceg, 2pteE, 3pte. These are also top double-blast hits. Scoring with t49.t98_2 puts 1cef=1ceg=3pte=2pteE on top (score -116.87), with 1blsA=1blsB=2bltA=2bltB a ways behind (-74.62). Nothing else scores particularly well, not even 1btl and 1pmd, which have significant structural similarity to 3pte. Note: 1btl does get the third highest score in the model library (at -7.74). With summing, 3pte gets -217.7 and 2bltA gets -165.05. It seems pretty obvious that 3pte (which is even in the t49.t98_2 alignment) is the right target to use. -------------------------------------------------- 16 July 1998 Kevin Karplus t49-3pte-post = t49-3pte-global 3pte-t49-post = 3pte-t49-global The alignments are very different: Largest difference: 3pte-t49-fssp t49-3pte-global 0.421645 best compromise? 3pte-t49-vit (worst match 3pte-t49-const 0.597562, best match 3pte-t49-global 0.885714) -------------------------------------------------- 17 July 1998 The 3pte-t49-vit alignment drops a lot off the end---stuff that seems to align just fine. I started over with 3pte-t49-global, which agreed largely with 3pte-t49-vit, then hand edited it to get 3pte-t49-hand. The first chunk was a helix that had several reasonable alignments---each a turn apart. I picked the alignment which resulted in the least insertion at the end. I also moved some gaps slightly so that a number of insertions and deletions clustered together on the surface. I decided to align some residues in the center to make the insertions be in the same place, even though the automatic alignments left them unaligned. I'm not sure which of the secondary structure predictions is better---they seem to be making very similar mistakes. I tried making another target98 alignment using my hand-alignment 3pte-t49-hand as a seed, but it quickly drifted away from t49, and so is not much use even for predicting secondary structure (it is aligned to 3pte, not t49 anyway).