Tue Jul 11 10:51:34 PDT 2000 Kevin Karplus T0109 Protein HI1715, H. influenzae wu-blastp: weak hits for 1pmt, 2pmt[ABCD], 1vdf[ABCDE] double-blast: no hits t2k: 33 sequences, none in PDB secondary structure: helical, with some beta strands CAFASP SAM-T99 hits: Summary of Database Hits: Average Target Template SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel 1pymA -8.51 4.509 --------- --------- -8.51 4.5 1qqtA -7.83 8.898 -7.83 8.9 --------- --------- Methionyl-tRNA Synthetase 1qhaA -7.61 11.09 --------- --------- -7.61 11 1dgkN -7.42 13.4 --------- --------- -7.42 13 1qfxA -7.25 15.89 --------- --------- -7.25 16 1cqxA -7.11 18.27 --------- --------- -7.11 18 1qj4A -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 1yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 2yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 3yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 4yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 5yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 6yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 7yasA -7.08 18.83 -7.08 19 --------- --------- Hydroxynitrile Lyase 1cw3A -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase 1cw3B -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase 1cw3C -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase 1cw3D -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase 1cw3E -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase 1cw3F -7 20.39 -7 20 --------- --------- Mitochondrial Aldehyde Dehydrogenase T99 target hits Chain E-value FSSP SCOP 1qqtA 8.9 1qqtA 1.28.1,3.19.1,7.39.1 1qj4A 19 1qj4A 3.64.1 [1-7]yasA 19 1qj4A 3.64.1 1cw3[ABCDEF] 20 1bpwA 3.76.1 T2K target hits: Chain E-value FSSP SCOP 1qqcA 0.97 1tgoA 3.50.3,5.8.1 1d5aA 7.9 1tgoA ? probably 3.50.3,5.8.1 1qqtA 11 1qqtA 1.28.1,3.19.1,7.39.1 template hits Chain E-value FSSP 1pymA -8.51 4.58 1pyma 3.1.23 1qhaA -7.61 11.2 1qhaA 3.50.1 1dgkN -7.42 13.6 1dgkN ? probably 3.50.1 1qfxA -7.25 16.1 1qfxA ? probably 3.55.1 1cqxA -7.11 18.5 1cqxA 1.1.1,2.41.1,3.18.1 2hgsA -6.77 26.0 2hgsA 3.25.1,4.121.1 1aa8A -6.71 27.6 1an9A 3.4.1,4.14.1 No bi-directional hits (except, maybe, fold 3.50) Tue Jul 18 12:07:32 PDT 2000 CAFASP hits 14 3.50.3 9 5.8.1 8 3.42.1 6 1.47.1 6 1.1.1 5 3.16.2 4 3.2.1 3.50.3 or 3.50.1 look like our best bets: 3.50.3: 1qqcA, 1tgoA, 1d5aA, 1xwl(from Genthreader) 3.50.1: 1qhaA, 1dgkN 15 August 2000 Christian (not properly sorted, sorry) [SORTED BY KARPLUS 31 Aug 2000] 1pymA/T0109-1pymA-2track-global.pw:1pymA 295 -7159.39 -23.59 3.1e-10 1pymA/T0109-1pymA-2track-local.pw:1pymA 295 -7172.82 -19.84 1.7e-08 1pymA/1pymA-T0109-global.pw:T0109 182 -4.94 -16.80 1.5e-07 1qj4A/T0109-1qj4A-2track-global.pw:1qj4A 257 -7144.04 -15.27 9.2e-07 1qqtA/T0109-1qqtA-2track-local.pw:1qqtA 551 -7176.72 -14.89 2.5e-06 1qj4A/T0109-1qj4A-2track-local.pw:1qj4A 257 -7154.74 -11.37 5.0e-05 1qj4A/1qj4A-T0109-fssp-global.pw:T0109 182 -5.92 -9.00 3.7e-04 1cqxA/1cqxA-T0109-vit.pw:T0109 182 -13.14 -8.89 4.1e-04 1pymA/1pymA-T0109-local.pw:T0109 182 -19.09 -8.59 5.6e-04 1qj4A/T0109-1qj4A-vit.pw:1qj4A 257 -11.69 -8.05 9.6e-04 1qqtA/T0109-1qqtA-local.pw:1qqtA 551 -18.58 -7.66 1.4e-03 1qhaA/1qhaA-T0109-local.pw:T0109 182 -20.41 -7.67 1.4e-03 1aa8A/1aa8A-T0109-vit.pw:T0109 182 -10.65 -7.52 1.6e-03 1dgkN/1dgkN-T0109-local.pw:T0109 182 -20.10 -7.47 1.7e-03 1qfxA/1qfxA-T0109-local.pw:T0109 182 -18.03 -7.38 1.9e-03 1dgkN/1dgkN-T0109-vit.pw:T0109 182 -11.06 -7.07 2.6e-03 1qhaA/1qhaA-T0109-vit.pw:T0109 182 -10.34 -6.91 3.0e-03 2hgsA/2hgsA-T0109-local.pw:T0109 182 -17.64 -6.79 3.4e-03 1aa8A/1aa8A-T0109-local.pw:T0109 182 -18.89 -6.67 3.8e-03 1tgoA/T0109-1tgoA-local.pw:1tgoA 773 -16.90 -6.20 6.1e-03 1cqxA/1cqxA-T0109-local.pw:T0109 182 -18.80 -6.07 6.9e-03 1tgoA/T0109-1tgoA-vit.pw:1tgoA 773 -9.21 -6.02 7.3e-03 1tgoA/T0109-1tgoA-2track-global.pw:1tgoA 773 -7085.88 -6.07 7.4e-03 1qfxA/1qfxA-T0109-vit.pw:T0109 182 -10.47 -5.82 8.9e-03 1cqxA/1cqxA-T0109-global.pw:T0109 182 -1.27 -5.62 1.1e-02 1qj4A/T0109-1qj4A-local.pw:1qj4A 257 -16.13 -5.50 1.2e-02 1qqtA/T0109-1qqtA-vit.pw:1qqtA 551 -10.18 -5.22 1.6e-02 2hgsA/2hgsA-T0109-vit.pw:T0109 182 -9.82 -5.11 1.8e-02 1pymA/1pymA-T0109-vit.pw:T0109 182 -8.80 -4.70 2.7e-02 1pymA/1pymA-T0109-fssp-global.pw:T0109 182 -14.61 -4.20 4.4e-02 1aa8A/T0109-1aa8A-2track-global.pw:1aa8A 340 -7118.82 -4.85 5.4e-02 1xwl/1xwl-T0109-vit.pw:T0109 182 -8.02 -3.32 1.0e-01 1tgoA/1tgoA-T0109-local.pw:T0109 182 -16.12 -3.06 1.3e-01 1xwl/1xwl-T0109-local.pw:T0109 182 -15.53 -2.96 1.5e-01 1qqtA/1qqtA-T0109-vit.pw:T0109 182 -8.41 -2.66 2.0e-01 1qfxA/T0109-1qfxA-2track-local.pw:1qfxA 441 -7169.55 -2.69 3.6e-01 1aa8A/T0109-1aa8A-2track-global.pw:1aa8A 347 -7111.78 -2.07 3.6e-01 1tgoA/1tgoA-T0109-vit.pw:T0109 182 -8.42 -1.44 5.8e-01 1qhaA/T0109-1qhaA-vit.pw:1qhaA 917 -4.72 -1.21 6.9e-01 1dgkN/T0109-1dgkN-vit.pw:1dgkN 917 -4.72 -1.21 6.9e-01 2hgsA/T0109-2hgsA-vit.pw:2hgsA 474 -3.50 -1.08 7.6e-01 1pymA/T0109-1pymA-local.pw:1pymA 295 -10.11 -0.48 1.1e+00 1aa8A/T0109-1aa8A-local.pw:1aa8A 347 -10.79 -0.52 1.1e+00 2hgsA/T0109-2hgsA-local.pw:2hgsA 474 -10.35 -0.45 1.2e+00 1qqtA/1qqtA-T0109-local.pw:T0109 182 -14.67 -0.37 1.2e+00 1aa8A/T0109-1aa8A-vit.pw:1aa8A 347 -4.01 -0.42 1.2e+00 1xwl/T0109-1xwl-vit.pw:1xwl 580 -3.98 -0.31 1.3e+00 1cqxA/T0109-1cqxA-vit.pw:1cqxA 403 -3.75 -0.21 1.3e+00 1xwl/T0109-1xwl-2track-local.pw:1xwl 580 -7179.20 0.69 1.5e+00 1qqtA/T0109-1qqtA-2track-global.pw:1qqtA 546 -7123.87 -0.75 1.5e+00 1qfxA/T0109-1qfxA-local.pw:1qfxA 460 -9.79 0.18 1.6e+00 1cqxA/T0109-1cqxA-local.pw:1cqxA 403 -10.42 0.16 1.6e+00 1qfxA/T0109-1qfxA-vit.pw:1qfxA 460 -2.93 0.25 1.7e+00 1qfxA/T0109-1qfxA-local.pw:1qfxA 441 -9.81 0.21 1.7e+00 1qhaA/T0109-1qhaA-local.pw:1qhaA 917 -10.99 0.44 1.8e+00 1xwl/T0109-1xwl-local.pw:1xwl 580 -10.63 0.50 1.9e+00 1qj4A/1qj4A-T0109-local.pw:T0109 182 -11.25 0.54 1.9e+00 1dgkN/T0109-1dgkN-local.pw:1dgkN 917 -10.98 0.70 2.0e+00 1dgkN/T0109-1dgkN-2track-local.pw:1dgkN 917 -7174.07 1.94 2.2e+00 1xwl/T0109-1xwl-2track-global.pw:1xwl 580 -7125.32 2.55 2.6e+00 1qj4A/1qj4A-T0109-vit.pw:T0109 182 -3.47 1.95 2.6e+00 1qfxA/T0109-1qfxA-2track-local.pw:1qfxA 460 -7163.77 2.60 2.6e+00 1pymA/T0109-1pymA-vit.pw:1pymA 295 -2.10 1.80 2.6e+00 1tgoA/T0109-1tgoA-2track-local.pw:1tgoA 773 -7169.56 4.00 2.9e+00 1qqtA/T0109-1qqtA-2track-global.pw:1qqtA 551 -7116.70 3.23 2.9e+00 1qfxA/T0109-1qfxA-2track-global.pw:1qfxA 441 -7120.08 4.89 2.9e+00 2hgsA/T0109-2hgsA-global.pw:2hgsA 474 38.60 1000000.00 3.0e+00 2hgsA/T0109-2hgsA-2track-local.pw:2hgsA 474 -7156.39 15.82 3.0e+00 2hgsA/T0109-2hgsA-2track-global.pw:2hgsA 474 -7110.23 11.47 3.0e+00 1qhaA/1qhaA-T0109-vit.pw Alignment is to a contiguous piece of 1qhaA, which is a much larger protein. Aligned structure is not compact. 2ary structure match is not so hot. 1tgoA/1tgoA-T0109-vit.pw Only aligns a short N-terminal portion of the target to the structure. 1tgoA/T0109-1tgoA-2track-global.pw Not a compact alignment, at all 1qqtA/T0109-1qqtA-2track-local.pw:1qqtA 551 -7176.72 -14.89 2.5e-06 Aligns to a 4-helix bundle and some structure on top of the bundle. The residue conservation is not great. Maybe worth looking at though. 1qj4A/T0109-1qj4A-vit.pw:1qj4A 257 -11.69 -8.05 9.6e-04 Just aligns a helix. 1qj4A/T0109-1qj4A-2track-global.pw:1qj4A 257 -7144.04 -15.27 9.2e-07 The secondary structure agreement may be better, but there are more glaring structural problems. Not the best alignment for this protein. 1qj4A/1qj4A-T0109-fssp-global.pw:T0109 182 -5.92 -9.00 3.7e-04 The secondary structure agreement isn't so hot and there are a couple of structural problems, but this is a possibility. Single chain protein, small, and does show some residue conservation. 1qhaA/1qhaA-T0109-vit.pw:T0109 182 -10.34 -6.91 3.0e-03 The entire target sequence is aligned to an extended piece of structure that is a small part of the large template protein. There is a little bit of interestin signal, but it's probably not meaningful. 1qfxA/1qfxA-T0109-vit.pw:T0109 182 -10.47 -5.82 8.9e-03 30 residue "alignment" 1pymA/1pymA-T0109-global.pw:T0109 182 -4.94 -16.80 1.5e-07 Covers a bit of structure, but it is too loose and jumps too much structure to be considered a decent alignment. 1pymA/T0109-1pymA-2track-global.pw:1pymA 295 -7159.39 -23.59 3.1e-10 Not much residue conservation, misses large chunks of structure. 1aa8A/1aa8A-T0109-vit.pw:T0109 182 -10.65 -7.52 1.6e-03 Aligns about 120 residues to an extended piece of structure. 1cqxA/1cqxA-T0109-vit.pw:T0109 182 -13.14 -8.89 4.1e-04 The last 90 residues of the target align to the template with some quite decent residue conservation. Worth looking at. 1dgkN/1dgkN-T0109-vit.pw:T0109 182 -11.06 -7.07 2.6e-03 Does have some residue conservation, but matches a very elongated (but contiguous) piece of structure from a much larger protein. 1pymA/1pymA-T0109-fssp-global.pw:T0109 182 -14.61 -4.20 4.4e-02 This one is worth further investigation, as the structural problems may not be fatal. The only possibilities so far: 1cqxA/1cqxA-T0109-vit.pw 1pymA-T0109-fssp-global.pw 1qj4A/1qj4A-T0109-fssp-global.pw 1qqtA/T0109-1qqtA-2track-local.pw:1qqtA Sat Aug 26 14:33:03 PDT 2000 Kevin Karplus Remade 2track predictions New top hits: % Sequence ID Length Simple Reverse E-value SCOP 2cmd 312 -27.78 -11.91 5.7e-02 3.2.1,4.140.1 1lbu 213 -20.79 -9.52 4.2e-01 1.21.1,4.52.1 1bdmA 327 -22.73 -8.93 1.1e+00 3.2.1,4.140.1 1a6q 382 -27.23 -8.65 1.1e+00 4.137.1 1bmdA 327 -22.51 -8.58 1.1e+00 3.2.1,4.140.1 1ceqA 316 -24.72 -8.56 1.1e+00 3.2.1,4.140.1 1bif 469 -28.65 -8.16 1.1e+00 3.31.1,3.55.1 Of these, only 3.2.1 came up (weakly) as a CAFASP hit. Still, we should try all our top hits. Thu Aug 31 14:57:57 PDT 2000 Kevin Karplus Top 22 alignments: 1bdmA/T0109-1bdmA-2track-global 1bdmA 317 -3.96 -29.76 7.6e-13 only 9 identical residues, missing chunks of fold 1bmdA/T0109-1bmdA-2track-global 1bmdA 327 -1.13 -28.07 2.1e-12 only 9 identical residues, missing chunks of fold 1qj4A/T0109-1qj4A-2track-global 1qj4A 257 -5.83 -27.54 5.6e-12 ok pieces, but gaps not closable, and missing big chunk of fold. 2cmd/T0109-2cmd-2track-global 2cmd 312 -3.83 -24.76 1.1e-10 22 identical residues, with some beta-pairing, but missing big chunks of fold. 1ceqA/T0109-1ceqA-2track-global 1ceqA 316 -0.78 -19.51 1.7e-08 very few identical residues, missing big chunks. 1pymA/1pymA-T0109-global T0109 182 -4.94 -16.80 1.5e-07 another non-compact one 2cmd/T0109-2cmd-2track-local 2cmd 312 -27.78 -11.91 5.0e-05 12 identical residues, missing most of fold. 1a6q/T0109-1a6q-2track-local 1a6q 363 -28.62 -9.63 3.7e-04 only 6 identical residues, missing most of fold. 1lbu/T0109-1lbu-2track-local 1lbu 213 -20.79 -9.52 3.7e-04 10 identical residues with some good 2ry match, but missing most of fold 1qj4A/1qj4A-T0109-fssp-global T0109 182 -5.92 -9.00 3.7e-04 20 identical residues in rather gappy alignment. Nice match for THSENGLIERIKASKLTERAA poo 2ry match. 1cqxA/1cqxA-T0109-vit T0109 182 -13.14 -8.89 4.1e-04 1pymA/1pymA-T0109-local T0109 182 -19.09 -8.59 5.6e-04 1qj4A/T0109-1qj4A-vit 1qj4A 256 -11.69 -8.05 9.6e-04 1a6q/T0109-1a6q-2track-local 1a6q 382 -27.23 -8.65 1.0e-03 1bdmA/T0109-1bdmA-2track-local 1bdmA 327 -22.73 -8.93 1.0e-03 1bif/T0109-1bif-2track-local 1bif 469 -28.65 -8.16 1.0e-03 1bmdA/T0109-1bmdA-2track-local 1bmdA 327 -22.51 -8.58 1.0e-03 1ceqA/T0109-1ceqA-2track-local 1ceqA 316 -24.72 -8.56 1.0e-03 1qhaA/1qhaA-T0109-local T0109 182 -20.41 -7.67 1.4e-03 matches some long helices, with 29 identical residues, but is a long skinny piece that crosses domain boundaries. Also, the few conserved residues in the T2K multiple alignment are not conserved in this alignment. An unconvincing match. 1qqtA/T0109-1qqtA-local 1qqtA 546 -18.59 -7.68 1.4e-03 1aa8A/1aa8A-T0109-vit T0109 182 -10.65 -7.52 1.6e-03 1dgkN/1dgkN-T0109-local T0109 182 -20.10 -7.47 1.7e-03 Thu Aug 31 16:27:30 PDT 2000 Kevin Karplus Let's look at function. Target is ORN_HAEIN, about which Swissprot says: 3'-to-5' exoribonuclease specific for small oligoribonucleotides, belongs ot oligoribonuclease family. ORN_ECOLI adds comment: homodimer. ORN_HUMAN, ORN_CAEEL, and ORN_YEAST add no new annotation. Gene names in yeast: YNT20 or LYR059C or L2159 PIR for YNT20 protein says Inactivation of YME2, which encodes an integral inner mitochondrial membrane protein, causes increased escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. (this description seems irrelevant, is it in the wrong part of PIR?) Several more ORN_* in swissprot, all of which are oligoribonucleotides by similarity. (Similiarity to what? I can't seem to find the one that was confirmed as an oligoribonucleotide.) Next set of hits in T2k alignment are all DNA Polymerase III, either epsilon chain or alpha subunit. Doing a simple search for keywords in fssp's TABLE2: The representatives in FSSP for ribonucleases are 1a4yA 3.9.1 1a6f 4.12.1 1ay7B 3.8.1 1azpA 4.8.1 1b20A 4.1.1 1bk7A 4.103.1 1bolA 4.103.1 1ckqA 3.47.1 1onc 4.5.1 1qhkA 4.84.1 1rgeA 4.1.1 1rthA 3.50.3,5.8.1 * 1yagA 3.50.1,3.50.1 * 2rn2 3.50.3 * 3dni 4.130.1 7rsa 4.5.1 9rnt 4.1.1 The representatives in FSSP for DNA polymerases are 1b77A 4.110.1,4.110.1 1bpyA 1.60.10,5.9.1 1clqA 3.50.3,5.8.1 * 1dmlA ? 1dmlB ? 1igtB 2.1.1,2.1.1,2.1.1,2.1.1 1t7pA 3.50.3,5.8.1 * 1taq 1.60.3,3.48.1 1tgoA 3.50.3,5.8.1 * 1thx 3.42.1 1xwl 3.50.3,5.8.1 * 8fabA 2.1.1,2.1.1 So the only fold that is shared by the known ribonucleases and the known DNA polymerases is 3.50.3 (or 3.50.1) and 5.8.1. These are the popular CAFASP predictions, so let's try again to get an alignment! Fri Sep 1 14:25:05 PDT 2000 Kevin Karplus The 12 FSSP representatives with 3.50.3 domains are 1b7eA 1b9dA 1bco 1clqA 1cxqA 1hjrA 1rthA 1t7pA 1taq 1tgoA 1xwl 2rn2 The 19 FSSP representatives with 3.50 domains are 1b7eA 1b9dA 1ba1 1bco 1chmA 1clqA 1cxqA 1glcG 1hjrA 1mgtA 1qhaA 1rthA 1sfe 1t7pA 1taq 1tgoA 1xwl 1yagA 2rn2 The 10 FSSP representatives with 5.8.1 domains are 1cezA 1clqA 1mml 1quvA 1rdr 1rthA 1t7pA 1taq 1tgoA 1xwl The 6 with both: 1clqA 1rthA 1t7pA 1taq 1tgoA 1xwl The 7 ribonuclease or DNA polymerase: 1clqA 1rthA 1t7pA 1tgoA 1xwl 1yagA 2rn2 I made joint models for all of these, and ranked them by reverse score. I've marked with a * those that have a 3.50 or 5.8.1 domain: 1bdmA/T0109-1bdmA-2track-global 1bdmA 317 -3.96 -29.76 7.6e-13 1bmdA/T0109-1bmdA-2track-global 1bmdA 327 -1.13 -28.07 2.1e-12 1qj4A/T0109-1qj4A-2track-global 1qj4A 257 -5.83 -27.54 5.6e-12 1hjrA/T0109-1hjrA-2track-global 1hjrA * 158 -10.04 -24.01 1.1e-10 1sfe/T0109-1sfe-2track-global 1sfe * 165 -8.99 -24.22 1.1e-10 2cmd/T0109-2cmd-2track-global 2cmd 312 -3.83 -24.76 1.1e-10 1ceqA/T0109-1ceqA-2track-global 1ceqA 316 -0.78 -19.51 1.7e-08 2rn2/T0109-2rn2-2track-global 2rn2 * 155 -4.80 -17.10 1.2e-07 1pymA/1pymA-T0109-global T0109 182 -4.94 -16.80 1.5e-07 1b9dA/T0109-1b9dA-2track-global 1b9dA * 143 -5.41 -16.83 3.4e-07 1cxqA/T0109-1cxqA-2track-global 1cxqA * 143 -3.06 -15.56 9.2e-07 2cmd/T0109-2cmd-2track-local 2cmd 312 -27.78 -11.91 5.0e-05 1mgtA/T0109-1mgtA-2track-global 1mgtA * 169 -5.53 -10.63 1.4e-04 1mml/1mml-T0109-global T0109 * 182 -1.42 -10.46 1.4e-04 1a6q/T0109-1a6q-2track-local 1a6q 363 -28.62 -9.63 3.7e-04 1lbu/T0109-1lbu-2track-local 1lbu 213 -20.79 -9.52 3.7e-04 1qj4A/1qj4A-T0109-fssp-global T0109 182 -5.92 -9.00 3.7e-04 1cqxA/1cqxA-T0109-vit T0109 182 -13.14 -8.89 4.1e-04 1pymA/1pymA-T0109-local T0109 182 -19.09 -8.59 5.6e-04 1qj4A/T0109-1qj4A-vit 1qj4A 256 -11.69 -8.05 9.6e-04 1a6q/T0109-1a6q-2track-local 1a6q 382 -27.23 -8.65 1.0e-03 1bdmA/T0109-1bdmA-2track-local 1bdmA 327 -22.73 -8.93 1.0e-03 1bif/T0109-1bif-2track-local 1bif 469 -28.65 -8.16 1.0e-03 1ceqA/T0109-1ceqA-2track-local 1ceqA 316 -24.72 -8.56 1.0e-03 1qhaA/1qhaA-T0109-local T0109 * 182 -20.41 -7.67 1.4e-03 1qqtA/T0109-1qqtA-local 1qqtA 546 -18.59 -7.68 1.4e-03 1aa8A/1aa8A-T0109-vit T0109 182 -10.65 -7.52 1.6e-03 1dgkN/1dgkN-T0109-local T0109 182 -20.10 -7.47 1.7e-03 1qfxA/1qfxA-T0109-local T0109 182 -18.03 -7.38 1.9e-03 1dgkN/1dgkN-T0109-vit T0109 182 -11.06 -7.07 2.6e-03 1ceqA/T0109-1ceqA-2track-local 1ceqA 304 -23.73 -7.17 2.7e-03 1qhaA/1qhaA-T0109-vit T0109 * 182 -10.34 -6.91 3.0e-03 2hgsA/2hgsA-T0109-local T0109 182 -17.64 -6.79 3.4e-03 1aa8A/1aa8A-T0109-local T0109 182 -18.89 -6.67 3.8e-03 1tgoA/T0109-1tgoA-local 1tgoA * 773 -16.90 -6.20 6.1e-03 1cqxA/1cqxA-T0109-local T0109 182 -18.80 -6.07 6.9e-03 1tgoA/T0109-1tgoA-vit 1tgoA * 773 -9.21 -6.02 7.3e-03 1qj4A/T0109-1qj4A-2track-local 1qj4A 256 -21.05 -6.93 7.4e-03 1t7pA/T0109-1t7pA-2track-local 1t7pA * 662 -25.82 -6.60 7.4e-03 1qfxA/1qfxA-T0109-vit T0109 182 -10.47 -5.82 8.9e-03 1hjrA/T0109-1hjrA-2track-global has 11 identical residues. Covers full domain with inserts in reasonable places. From: Rachel Karchin I've tried to put some comments in the README for t109 but I see you're editing it as well so I'm sending mail to avoid stomping on your changes. Have you looked at 1hjrA/T0109-1hjrA-2track-global yet? It looks pretty good. Almost the whole protein is aligned except for one helix and a small piece of another. 1sfe/T0109-1sfe-2track-global has 15 identical residues (after adjusting misaligned PDB atom sequence--> 1sfe/T0109-1sfe-karplus1.a2m). Covers full domain with inserts in reasonable places. One large gap, that would be easy to close. This looks better to me than 1hjrA With hand editing, the number of identical residues can be increased to 18, with some cost to the 2ry structure alignment. 1sfe/T0109-1sfe-karplus2.a2m On both alignments there is a helix predicted between the first two strands, which is not really compatible with the tight antiparallel turn. 2rn2/T0109-2rn2-2track-global has 12 identical residues. The one large gap would be difficult close, and one long mid-helix insertion predicts two other helices. That can be changed to a 3 -3helix insertion in a loop region (2rn2/T0109-2rn2-karplus1.a2m) This also has the problem of a predicted helix inserted between the first two strands. 1b9dA/T0109-1b9dA-2track-global has 10 identical residues inserts are mostly in reasonable places (again the helix between the first two strands). Light eidting increases the number of identical residues to 13: 1b9dA/T0109-1b9dA-karplus1.a2m 1b9dA does better on the beta sheet, but overall, I may still prefer 1sfe. 1cxqA/T0109-1cxqA-2track-global after editing to fix inconsistent alignments gets 17 identical residues, and has the best beta sheet I've seen yet. With a little more editing I get 25 identical residues, with no really nasty gaps or inserts (several little ones, and one big helical insert that is easy to believe). 1cxqA/T0109-1cxqa-karplus1.a2m 1mgtA/T0109-1mgtA-2track-global has 18 identical residues, but has the problem with the helix between the first two strands. Otherwise not bad. 1mml/1mml-T0109-global has 22 identical residues, before tweaking! But it has nasty, uncloseable gaps. 1qhaA/1qhaA-T0109-local has 29 identical residues, but is not compact in 3D and crosses domain boundaries. Even as a homodimer, it is not very convincing. Tue Sep 5 10:35:22 PDT 2000 remaking 2track t109 Sep 1 1cxqA 3.50.3.2.1 SUBMITTED T0109-1cxqA-karplus1 Mon Nov 27 13:24:24 PST 2000 Fold 3.50 is correct. I don't know yet about alignment.