Mon Jul 24 21:23:29 PDT 2000 Kevin Karplus T0116 MutS, Thermus Aquaticus DNA mismatch repair protein wu-blast: weak hit to 1dgcA, very weak to 1a8h, 2dgcA, 9ant[AB] double-blast: weak hits to 1se[rst][AB], 1sry[AB], 1dlxA t2k 151 sequences, none in PDB. 2ry prediction has both strands and helices---a lot of long helices Tue Jul 25 05:48:47 PDT 2000 Kevin Karplus Best scores: E-value FSSP SCOP 2reb 5.4e-05 2reb 3.31.1 2reb_1 4.4e-04 2reb 3.31.1,4.40.1 1cr1A 4.0e-03 1cr1A 3.31.1 1ng1 0.076 1ng1 1.30.1,3.31.1 1ypsA 0.243 ? ? Theoretical model 1bkdS 0.53 1bkdS 1.109.1 1b0uA 0.77 1b0uA 3.31.1 2shkA 2.55 1shkA 3.31.1 1qksA 3.73 1qksA 1.3.1,2.65.2 It seems pretty clear that there is a 3.31.1 domain (at least, the template models for that all match well). None of the top hits score well with both target and template. The target model does not get as good hits as the template models---only 1ypsA and 1bkdS are on the list above. The next set of hits are 1dv[36][LR] 6.5 6prcL ? 1aij[LR] 6.5 6prcL 6.2.1 [24]rcrL 6.5 6prcL 6.2.1 1pcrL 6.5 6prcL 6.2.1 1mpsL 6.5 6prcL 6.2.1 1e14L 6.5 ? ? 1aig[NL] 6.5 6prcL 6.2.1 1qovL 6.5 6prcL 6.2.1 1ds8[LR] 6.5 6prcL ? These are all within about 2 Angstroms of each other over 240 residues, with residue ids over 50%. There are t99 models for 6prcL and 1aijL. (It isn't clear whether the E-value should be 6.5 or 5.4---I get different numbers from the two scoring runs. Are they using different hmmscore parameters?) Top-scoring alignments are 2reb/2reb-T0116-local -31.98 -19.91 6.8e-09 2reb/2reb-T0116-global -11.16 -19.41 1.1e-08 2reb/2reb-T0116-vit -23.34 -19.43 1.1e-08 1cr1A/1cr1A-T0116-fssp-global -34.39 -17.88 5.2e-08 1cr1A/1cr1A-T0116-global -15.94 -16.08 3.1e-07 1cr1A/1cr1A-T0116-local -28.59 -15.30 6.8e-07 1cr1A/1cr1A-T0116-vit -19.54 -14.13 2.2e-06 1b0uA/1b0uA-T0116-fssp-global -26.27 -13.93 2.7e-06 1ng1/1ng1-T0116-local -25.15 -13.55 3.9e-06 1ng1/1ng1-T0116-global -6.30 -12.82 8.1e-06 1bkdS/T0116-1bkdS-local -30.98 -11.57 2.8e-05 1bkdS/T0116-1bkdS-local -30.98 -11.57 2.8e-05 2reb/2reb-T0116-fssp-global -28.53 -11.60 2.8e-05 1qksA/1qksA-T0116-local -20.62 -8.76 4.7e-04 1ng1/1ng1-T0116-vit -12.24 -8.56 5.8e-04 1aijL/T0116-1aijL-local -21.36 -8.16 8.6e-04 1aijL/T0116-1aijL-local -21.36 -8.16 8.6e-04 2shkA/2shkA-T0116-local -24.12 -8.06 9.5e-04 1b0uA/1b0uA-T0116-local -22.86 -7.92 1.1e-03 1cr1A/T0116-1cr1A-vit -11.13 -7.46 1.7e-03 Some of these scores look quite good, so we can expect at least a domain match. With 811 residues, we probably need to split the sequence into domains and do a separate search for each domain. The 2reb match is for 150-200 residues near the C-terminus. The 1bkdS match is for a larger domain near the N-terminus. Tue Jul 25 13:55:54 PDT 2000 2reb/2reb-T0116-local is a nice EHEHEHEHE alternation, making 5-strand sheet. Gaps are in reasonable places. 2reb/2reb-T0116-global may be slightly over-aligned, but the extension to cover 6 strands of the domain seems reasonable. 2reb/2reb-T0116-vit looks very much like 2reb/2reb-T0116-local Wed Jul 26 11:59:47 PDT 2000 The SAM-T99 (on CAFASP) target model gets chain E-value FSSP SCOP 1fokA 0.11 2fokA 1.4.4.10.1 1bkdS 0.86 1bkdS 1.109.1 1gpmA 1.01 1gpmA 3.19.2,3.63.1,4.44.2 2fokA 1.15 2fokA 1.4.4.10.1 1tmo 2.2 1dmr 2.49.2, 3.75.1 1qlaA 3.2 1qlaA 1.7.4, 3.3.1, 4.146.1 1a4yA 3.6 1a4yA 3.9.1 1b6cB 4.4 1b6cB 4.123.1 1dkvA 5.4 1dkvA 1.41.1, 2.13.1, 4.3.1 1db1A 7.7 1db1A 1.115.1 1cl1A 8.2 1cl2A 3.62.1 1cc0E 8.8 1rhoA ? 2.1.1 still no 2-way hits. 14 August 2000 Christian 1cr1A/1cr1A-T0116-fssp-global -34.39 -17.88 5.2e-08 The alignment is to the latter half of the target sequence, but is more spotty and missing more important core regions than the 2reb alignments. 1b0uA/1b0uA-T0116-fssp-global -26.27 -13.93 2.7e-06 Similar comments as 1cr1A above. 1ng1/1ng1-T0116-local -25.15 -13.55 3.9e-06 Not a compact alignment. 1qksA/1qksA-T0116-local -20.62 -8.76 4.7e-04 This is an interesting hit. Even though it is a local alignment, the first part of the target sequence is aligned to a fair bit of 1qks. 1aijL/T0116-1aijL-local -21.36 -8.16 8.6e-04 Non-compact alignment to some helices. 2shkA/2shkA-T0116-local -24.12 -8.06 9.5e-04 Spotty alignment. Not interesting. 1b0uA/1b0uA-T0116-local -22.86 -7.92 1.1e-03 I think most of the signal on this one is coming from a a conserved 7-contiguous-residue match. 1cr1A/T0116-1cr1A-vit -11.13 -7.46 1.7e-03 Spotty and short alignment. Not interesting. Sat Aug 26 15:04:32 PDT 2000 Kevin Karplus Remade 2track predictions Some strong hits: % Sequence ID Length Simple Reverse E-value SCOP 1tgoA 773 -79.87 -36.81 7.9e-13 3.50.3,5.8.1 1qlaA 656 -60.80 -25.83 4.8e-08 1.7.4,3.3.1,4,146.1 1cl2A 395 -47.50 -24.96 1.3e-07 3.62.1 1dg3A 592 -79.96 -24.69 1.3e-07 1.106.1,3.31.1 1cl1A 395 -45.86 -22.60 9.5e-07 3.62.1 1clqA 903 -72.93 -19.91 1.9e-05 3.50.3,5.8.1 1cjaA 342 -47.23 -19.17 1.9e-05 4.123.1 1gln 468 -50.73 -18.70 5.2e-05 1.92.1,3.19.1 1lox 662 -49.51 -18.57 5.2e-05 1.111.1,2.11.1 1qmmA 961 -59.17 -17.84 1.4e-04 1.110.1,2.6.1,4.13.4,4.123.1 1qltA 560 -42.96 -17.46 1.4e-04 4.48.27,4.124.1 The 3.31.1 match has dropped to second place, and the 6.2.1 matches have disappeared entirely. The 3.31.1 match is a bit more promising now, since that was previously only found with template models, not target models. Sun Aug 27 13:13:20 PDT 2000 The top-scoring alignments are now 1dg3A/T0116-1dg3A-2track-global 1dg3A 592 -60.82 -45.03 8.6e-20 1tgoA/T0116-1tgoA-2track-global 1tgoA 773 -44.84 -36.23 7.0e-16 1tgoA/T0116-1tgoA-2track-local 1tgoA 773 -79.87 -36.81 7.0e-16 1clqA/T0116-1clqA-2track-global 1clqA 903 -47.11 -31.49 1.0e-13 1qlaA/T0116-1qlaA-2track-local 1qlaA 655 -60.80 -25.83 4.2e-11 1cl2A/T0116-1cl2A-2track-local 1cl2A 391 -47.51 -24.97 1.1e-10 1dg3A/T0116-1dg3A-2track-local 1dg3A 592 -79.96 -24.69 1.1e-10 1cl1A/T0116-1cl1A-2track-local 1cl1A 391 -45.87 -22.60 8.4e-10 2reb/2reb-T0116-local T0116 811 -31.98 -19.91 6.8e-09 2reb/2reb-T0116-global T0116 811 -11.16 -19.41 1.1e-08 2reb/2reb-T0116-vit T0116 811 -23.34 -19.43 1.1e-08 1clqA/T0116-1clqA-2track-local 1clqA 903 -72.93 -19.91 1.7e-08 1cr1A/1cr1A-T0116-fssp-global T0116 811 -34.39 -17.88 5.2e-08 1cr1A/1cr1A-T0116-global T0116 811 -15.94 -16.08 3.1e-07 1cr1A/1cr1A-T0116-local T0116 811 -28.59 -15.30 6.8e-07 1cr1A/1cr1A-T0116-vit T0116 811 -19.54 -14.13 2.2e-06 1b0uA/1b0uA-T0116-fssp-global T0116 811 -26.27 -13.93 2.7e-06 1ng1/1ng1-T0116-local T0116 811 -25.15 -13.55 3.9e-06 1ng1/1ng1-T0116-global T0116 811 -6.30 -12.82 8.1e-06 The T0116-1dg3A-2track-global alignment has good 2ry structure matches, but the insertions and deletions are rather large, and the residue identity is rather low. Some hand-editing would be needed to get the incomplete PDB atom sequence aligned with the PDB SEQRES sequence. Despite the good 2-track score, I'm not sure this is a good hit. Although some pieces of 1tgoA/T0116-1tgoA-2track-global look ok, overall the alignment is too gappy to be convincing. 1tgoA/T0116-1tgoA-2track-local pulls out some good parts, but leaves large gaps---again not too convincing. 1clqA/T0116-1clqA-2track-global has got some good subdomains that seem to match---the DNA-binding makes this a more interesting candidate. Still a rather gappy alignment. 1qlaA/T0116-1qlaA-2track-local has some very good helix and sheet matches, but is again missing big chunks. It is clear that T0116 is multi-domain, and it might help if we could split it up into domains. 28 Aug 2000 Kevin Karplus It looks like 2reb domain is approximately 576 on (AHELVLI...) It may be that the 1bkdS domain is up to about 470. Let's try a 3-way overlapping split: 1-500, 400-600, 500-end. The 1-500 chunk may need to be split again. 1-500: The (weak) double-blast hits for 1-500 are 1dkg[AB] 0.012 2.68.1, 8.1.9 1dlxA 0.013 4.67.1 Target model hits are T0116-1-500 9ldt[AB] 2.8e+00 3.2.1,4.140.1 FSSP: 3ldh 9.8.1 T0116-1-500 9ldb[AB] 2.8e+00 3.2.1,4.140.1 FSSP: 3ldh 9.8.1 T0116-1-500 1cf2[OPRQ] 7.7e+00 ? T0116-1-500 1cfr 7.7e+00 3.47.1 T0116-1-500 1f83A 7.7e+00 ? T0116-1-500 1f82A 7.7e+00 ? SAM-T99 target+template top scores: Structure AverageReverse AverageEValue TargetReverse TargetEValue TemplateReverse TemplateEValue 1qksA -9.64 0.57 -- -- -9.64 1.1e+00 1.3.1,2.65.2 9ldtA -9.18 0.90 -9.18 1.1e+00 -- -- 3.2.1,4.140.1 1cf2O -9.13 0.95 -9.13 1.1e+00 -- -- ? 1cfr -8.50 1.78 -8.50 2.9e+00 -- -- 3.47.1 1ch6A -7.74 3.80 -7.74 8.0e+00 -- -- 3.2.1,3.53.1 1xwl -7.39 5.39 -- -- -7.39 8.0e+00 3.50.3,5.8.1 1ddqA -7.26 6.13 -7.26 8.0e+00 -- -- 9.6.1 Having 3.2.1 match twice in different contexts is interesting---it mayh be worth checking whether the 9ldtA and 1ch6A alignments agree on where the 3.2.1 domain is. Top 2-track hits: % Sequence ID Length Simple Reverse E-value SCOP 1tgoA 773 -69.01 -30.46 3.2e-10 3.50.3,5.8.1 1dg3A 592 -62.56 -23.80 3.5e-07 1.106.1,3.31.1 1qlaA 656 -49.32 -21.10 2.6e-06 1.7.4,3.3.1,4.146.1 1cjaA 342 -45.43 -19.49 1.9e-05 4.123.1 1t7pA 698 -62.46 -19.34 1.9e-05 3.50.3,5.8.1 1gpmA 525 -47.38 -19.07 1.9e-05 3.19.2,.63.1,4.44.2 1lox 662 -45.57 -17.60 1.4e-04 1.111.1,2.11.1 1cl2A 395 -38.51 -17.16 1.4e-04 3.62.1 1cl1A 395 -38.04 -17.11 1.4e-04 3.62.1 1ddzA 496 -45.03 -16.21 3.8e-04 ? 1b25A 619 -40.22 -16.14 3.8e-04 1.103.1,4.131.1 The 3.50.3 domain is particularly interesting, since it came up in both directions (1xwl template and 1tgoA 2track). If they agree on the location, it may be worth splitting there. Strongest alignments: name seq len simple rev e-value residues 1tgoA/T0116-1-500-1tgoA-2track-local 1tgoA 773 -69.01 -30.46 2.8e-13 67-494 1tgoA/T0116-1-500-1tgoA-2track-global 1tgoA 773 -28.42 -29.19 7.6e-13 26-500 1ch6A/T0116-1-500-1ch6A-2track-global 1ch6A 501 -24.22 -21.78 2.3e-09 scattered 1xwl/T0116-1-500-1xwl-2track-global 1xwl 580 -27.79 -13.72 6.8e-06 117-500 1xwl/T0116-1-500-1xwl-2track-local 1xwl 580 -47.06 -13.11 6.8e-06 299-432 3ldh/T0116-1-500-3ldh-2track-global 3ldh 330 -12.92 -10.20 1.4e-04 49-500 1qksA/1qksA-T0116-1-500-local T0116-1-500 500 -21.10 -9.67 3.7e-04 134-280 1ch6A/T0116-1-500-1ch6A-2track-local 1ch6A 501 -35.57 -7.64 2.7e-03 350-435,478-498 1qksA/1qksA-T0116-1-500-vit T0116-1-500 500 -10.81 -7.06 2.7e-03 153-277 1xwl/1xwl-T0116-1-500-local T0116-1-500 500 -19.67 -7.77 2.7e-03 216-433 Residue ranges: templ-local targ-local 2-track-local 1tgoA 13-442 tiny 67-494 (big inserts) 1xwl 220-433 all-gap 299-432 1ch6A all-gap 90-242 350-436,477-498 3ldh 317-412 52-169 151-233 (big insert) 1qksA 134-280 tiny 350-416 There's not much consistency in where the ones that supposedly share domains put the domains. 400-600: Only very weak blast hits and no double-blast hits. Target model hits: T0116-400-600 1gog 2.1e+01 2.1.1,2.17.1,2.64.1 T0116-400-600 1goh 2.1e+01 2.1.1,2.17.1,2.64.1 T0116-400-600 1gof 2.1e+01 2.1.1,2.17.1,2.64.1 Template hits: 1cr1A 0.15 3.31.1 2reb_1 1.20 3.31.1 2reb 1.57 3.31.1,4.40.1 1f2tA 2.54 ? 1b0uA 2.84 3.31.1 1ckeA 8.19 3.31.1 1ng1 8.61 1.30.1,3.31.1 2track hits: % ID Length Simple Reverse E-value SCOP 1cd1A 315 -40.74 -11.24 5.7e-02 2.1.1,4.17.1 1ek9A 428 -47.81 -10.66 1.6e-01 ? 2bmhA 455 -30.89 -9.84 4.2e-01 1.99.1 1bu7A 455 -32.08 -9.81 4.2e-01 1.99.1 2cgpA 210 -33.70 -9.76 4.2e-01 ? 1oxa 403 -34.05 -9.74 4.2e-01 1.99.1 1bp7A 152 -25.15 -9.11 4.2e-01 4.79.2 These hits look like they are just partial hits for the final domain (may be worth double-checking). 500-end: Only very weak blast hits and no double-blast hits. Target model hits: T0116-500-end 1qhlA 7.7e+00 T0116-500-end 1f2uA 7.7e+00 T0116-500-end 1f2tA 7.7e+00 T0116-500-end 1f2uC 7.7e+00 T0116-500-end 1gky 2.1e+01 T0116-500-end 1ayl 2.1e+01 T0116-500-end 1aq2 2.1e+01 SAM-T99 target&template hits Structure AvgReverse AvgEValue TargetReverse TargetEValue TemplateReverse TemplateEValue 1cr1A -18.84 5.7e-05 -- -- -18.84 1.3e-04 2reb -13.6 0.01 -5.28 5.8e+01 -21.92 6.6e-06 1ng1 -12.92 0.02 -- -- -12.92 5.4e-02 2reb_1 -12.57 0.03 -6.10 2.2e+01 -19.04 4.9e-05 1b0uA -11.47 0.09 -- -- -11.47 1.5e-01 1d6jA -11.29 0.11 -- -- -11.29 1.5e-01 The 2reb hit looks very strong and the 1cr1A hit looks ok. 2-track hits: % Sequence ID Length Simple Reverse E-value SCOP 1be3B 439 -35.03 -14.93 2.8e-03 4.111.1 1b0uA 262 -32.63 -14.80 2.8e-03 3.31.1 1ehyA 294 -30.54 -14.25 2.8e-03 3.64.1 1bw9A 356 -32.76 -13.83 7.7e-03 3.2.1,3.53.1 2reb 352 -31.31 -13.09 7.7e-03 3.31.1,1.40.1 1brwA 433 -33.16 -12.59 2.1e-02 1.48.2,3.20.1,4.35.1 This is more mixed, but there is still support for 3.31.1. Top alignments for 500-end: 1b0uA/T0116-500-end-1b0uA-2track-global 1b0uA 262 -12.99 -28.52 2.1e-12 1cr1A/1cr1A-T0116-500-end-global T0116-500-end 311 -17.10 -26.03 1.5e-11 2reb/2reb-T0116-500-end-global T0116-500-end 311 -19.22 -25.05 4.2e-11 2reb/T0116-500-end-2reb-global 2reb 352 -1.66 -24.28 1.1e-10 2reb/2reb-T0116-500-end-local T0116-500-end 311 -32.95 -22.08 8.4e-10 1b0uA/1b0uA-T0116-500-end-global T0116-500-end 311 -10.84 -21.09 2.3e-09 2reb/2reb-T0116-500-end-vit T0116-500-end 311 -24.30 -21.31 2.3e-09 2reb/T0116-500-end-2reb-2track-local 2reb 303 -41.21 -21.14 2.3e-09 1b0uA/1b0uA-T0116-500-end-fssp-global T0116-500-end 311 -21.13 -20.19 6.2e-09 2reb/T0116-500-end-2reb-2track-global 2reb 352 -21.37 -20.46 6.2e-09 1ng1/1ng1-T0116-500-end-global T0116-500-end 311 -11.49 -19.79 1.7e-08 These alignments score better than the ones done for the whole sequence--one of them should probably be used for this domain prediction. Looking at the 2reb, 1b0uA, and 1cr1A alignments, the domain starts around 525-545, with the 2reb alignments starting the earliest. Tue Aug 29 13:16:34 PDT 2000 Kevin Karplus 1b0uA/T0116-500-end-1b0uA-2track-global looks pretty good. The target has two substantial deletions, but the resulting gaps are fairly easily closed. After looking at 1b0uA/1b0uA-T0116-500-end-global, I hand edited to create T0116-500-end-1b0uA-karplus.a2m The final helices are a bit arbitrary, and may well be completely wrong. 1cr1A/1cr1A-T0116-500-end-global.pw has the same two deletions, but but has more little gaps than 1b0uA. 2reb/2reb-T0116-500-end-global.pw has some large insertions. Given the shortage of time, let's go with T0116-500-end-1b0uA-karplus.a2m I'm trying to split up the first 500 into 1-300 and 201-500 in hopes of finding something we can predict. Wed Aug 30 11:15:28 PDT 2000 Kevin Karplus T0116-1-300 no blast or double-blast hits 106 sequences in multiple alignment Top target hits: 9ld[bt][AB] 3.2.1,4.140.1 1fcpA 6.4.3 1qffA ? 1bf[ij] 4.77.1 1qadA 4.77.1 1picA 4.77.1 Top template (and target) hits ID avg target template SCOP 1qksA -10.41 0.26 -- -- -10.41 4.0e-01 1.3.1,2.65.1 1cq3A -7.68 4.03 -7.68 8.0e+00 -- -- 2.26.1 1oneA -7.53 4.68 -- -- -7.53 8.0e+00 3.1.10,4.45.1 9ldtA -7.36 5.55 -7.36 8.0e+00 -- -- 3.2.1,4.140.1 2tpsA -7.12 7.05 -- -- -7.12 8.0e+00 3.1.3 1bfi -7.10 7.20 -7.10 8.0e+00 -- -- 4.77.1 1qadA -7.09 7.27 -7.09 8.0e+00 -- -- 4.77.1 1picA -7.08 7.34 -7.08 8.0e+00 -- -- 4.77.1 1pssL -6.92 8.61 -6.92 2.2e+01 -- -- 6.2.1 1ystL -6.87 9.06 -6.87 2.2e+01 -- -- 6.2.1 1e14L -6.78 9.91 -6.78 2.2e+01 -- -- ? (note: script seems to use different parameters than the direct Makefile search, getting 1cq3A before 9ldtA) Top 2track hits: % Sequence ID Length Simple Reverse E-value SCOP 1cl2A 395 -40.48 -22.73 9.5e-07 3.62.1 1cl1A 395 -39.62 -22.44 9.5e-07 3.62.1 1tgoA 773 -41.33 -18.68 5.2e-05 3.50.3,5.8.1 1b8aA 438 -36.95 -16.21 3.8e-04 2.38.1,4.87.1 1cxqA 162 -31.26 -16.17 3.8e-04 3.50.3 1t7pA 698 -37.55 -16.00 3.8e-04 3.50.3,5.8.1 1b9dA 163 -31.88 -15.36 1.0e-03 3.50.3 1asu 162 -31.21 -15.32 1.0e-03 3.50.3 No consensus. Don't have time to look at so many differing predictions. T0116-201-500 Weak blast hits: 1dgcA, 2dgcA, 1a8h, 1ffkI no double-blast hits 115 sequences in T2k alignment 1 target hit: 1cfr 0.42 3.47.1 no 2-way hits 1cfr -9.95 0.42 -9.95 1.1e+00 -- -- 3.47.1 1xwl -7.66 4.11 -- -- -7.66 8.0e+00 3.50.3,5.8.1 1aipE -6.99 8.03 -- -- -6.99 2.2e+01 2.41.3,2.42.1,3.31.1 1a6q -6.48 13.37 -6.48 2.2e+01 -- -- 4.137.1 1b6cB -6.48 13.37 -6.48 2.2e+01 -- -- 4.123.1 1ddqA -6.46 13.64 -6.46 2.2e+01 -- -- 9.6.1 1ebhA_1 -6.46 13.64 -- -- -6.46 2.2e+01 3.1.10 1ojt -6.37 14.92 -6.37 2.2e+01 -- -- 3.3.1,4.72.1 4ubpC -6.26 16.65 -- -- -6.26 2.2e+01 ? 1bhy -6.23 17.16 -6.23 2.2e+01 -- -- 3.3.1,4.72.1 2oneA -6.12 19.15 -- -- -6.12 2.2e+01 3.1.10,4.45.1 1qhsA -6.05 20.53 -- -- -6.05 2.2e+01 ? Top 2-track hits: % Sequence ID Length Simple Reverse E-value X count 1b3qA 379 -35.60 -13.22 7.7e-03 1.31.2,2.38.6,4.101.1 1fiy 883 -44.06 -12.50 2.1e-02 3.1.11 1ddzA 496 -38.22 -12.48 2.1e-02 ? 1tgoA 773 -42.15 -12.13 2.1e-02 3.50.3,5.8.1 1dw9A 157 -29.61 -12.04 2.1e-02 ? 1qmmA 961 -40.55 -11.31 5.7e-02 1.110.1,2.6.1,4.13.3,4.123.1 1d1dA 262 -33.25 -11.24 5.7e-02 1.29.3,1.71.1 1ll1 590 -32.21 -11.11 5.7e-02 1.81.1,1.82.1,2.1.1 3.50.03 comes up in both directions, and 1tgoA also scored well on 1-300. Probably we should go with one of the 1tgoA alignments for T0116-1-500. Thu Aug 31 14:02:01 PDT 2000 Kevin Karplus t116-1-500/1tgoA/T0116-1-500-1tgoA-2track-local 1tgoA 773 -69.01 -30.46 2.8e-13 t116-1-500/1tgoA/T0116-1-500-1tgoA-2track-global 1tgoA 773 -28.42 -29.19 7.6e-13 t116-1-500/1tgoA/T0116-1-500-1tgoA-global 1tgoA 773 -3.72 -5.03 2.0e-02 t116-1-500/1tgoA/T0116-1-500-1tgoA-vit 1tgoA 773 -13.84 -1.88 8.1e-01 t116-1-500/1tgoA/T0116-1-500-1tgoA-local 1tgoA 773 -22.55 -0.54 1.5e+00 t116-1-500/1tgoA/1tgoA-T0116-1-500-local T0116-1-500 500 -18.92 1.69 2.2e+00 t116-1-500/1tgoA/1tgoA-T0116-1-500-vit T0116-1-500 500 -10.09 2.78 2.6e+00 t116-1-500/1tgoA/1tgoA-T0116-1-500-fssp-global T0116-1-500 500 17.06 1000000.00 3.0e+00 t116-1-500/1tgoA/1tgoA-T0116-1-500-global T0116-1-500 500 10.62 1000000.00 3.0e+00 T0116-1-500-1tgoA-2track-local has 35 identical residues, but is not very compact. The best conservation is at the N-terminus. T0116-1-500-1tgoA-2track-global has 33 identical residues, and is also not compact. T0116-1-500-1tgoA-global has 41 identical residues, but is split into two pieces that are widely separated, one at the C-terminus and one at the N-terminus. The larger C-terminus piece actually loks reasonably complete and compact. T0116-1-500-1tgoA-local is basically empty. 1tgoA-T0116-1-500-local is too short to be useful. I grabbed the ok part of T0116-1-500-1tgoA-global and put it in T0116-1-500-1tgoA-tweaked.a2m I don't really believe it, but I don't have anything better to offer. Wed Nov 29 It looks like there is a DNA-binding domain 1-120, that does not match any older PDB file (according to FSSP). The second domain 126-233 matches 1tgoA. Our alignment is 206-454 (much too late). The third domain 267-719 matched 1fnnA.