Wed Jul 26 11:32:18 PDT 2000 Kevin Karplus T0117 Deoxyribonucleoside kinase, Drosophila melanogaster Documentation says: Homodimer, distantly related to Herpes thymidine kinase. Homologous sequence of known structure. Herpes Thymidine Kinase is 1vtk, 2ki5B, 1ki2B, 1ki6A, 1qhiB, ... SCOP 3.31.1.1.6 FSSP 1qhiA But that doesn't come up in the t2k alignments. Instead we get KITH_VZVD KITH_HSVSA KITH_HSVBH KITH_HSVI1 pir:KIBETE KITH_VZVW KITH_VZV7 ... (Why doesn't PDB sequence appear?) wu-blast finds weak hit to 1qcrH double-blast finds moderate hit to 1ap0 t2k alignment has 80 sequences, none in PDB. Secondary structure prediction seems to be alternating helices and strands, usually with two helices between strands. Target model gets excllent hits on 2ki5[AB] 8.0e-35 1qhiA 3.31.1.1.6 1kim[AB] 8.0e-35 1qhiA 3.31.1.1.6 1qhi[AB] 8.0e-35 1qhiA 3.31.1.1.6 [123]vtk 8.1e-35 1qhiA 3.31.1.1.6 1ki[234678][AB] 1.7e-34 1qhiA 3.31.1.1.6 The top alignments with 1qhiA are 1qhiA/T0117-1qhiA-local 1qhiA 366 -98.58 -88.52 1.1e-38 1qhiA/T0117-1qhiA-global 1qhiA 300 -69.56 -87.01 4.9e-38 1qhiA/T0117-1qhiA-vit 1qhiA 366 -93.06 -86.76 6.3e-38 1qhiA/1qhiA-T0117-global T0117 250 -40.11 -49.42 1.0e-21 1qhiA/1qhiA-T0117-local T0117 250 -50.50 -39.50 2.1e-17 1qhiA/1qhiA-T0117-vit T0117 250 -39.93 -36.33 5.0e-16 1qhiA/1qhiA-T0117-fssp-global T0117 250 -27.62 -31.60 5.7e-14 1qhiA/T0117-1qhiA-local misses an edge strand of the beta sheet and has some truncation of helices 1qhiA/T0117-1qhiA-global seems similar 1qhiA/1qhiA-T0117-global is more complete, and has reasonable gaps, though the alignment of RRP in the center is rather dubious. 1qhiA/1qhiA-T0117-fssp-global seems similar. We'll probably want to compare the alignments with measure-shift and pick out the best one. Top 2-way hits are id e-value FSSP SCOP 3vtk 4.6e-24 1qhiA 3.31.1.1.6 1kimA 4.7e-24 1qhiA 3.31.1.1.6 1qhiA 6.2e-24 1qhiA 3.31.1.1.6 5tmpA 1.7e-20 5tmpA 3.31.1.1.16 3tmkA 1.5e-17 3tmkA 3.31.1.1.15 2tmkA 2.3e-15 3tmkA 3.31.1.1.15 5ukdA 7.8e-10 1zin 3.31.1.1.5 3adk 2.3e-09 1zin 3.31.1.1.7 1ukz 5.5e-09 1zin 3.31.1.1.2 1nksA 1.4e-05 1nksA 3.31.1.1.8 1ckeA 2.3e-04 1ckeA 3.31.1.1.4 2ak3A 1.4e-03 1zin 3.31.1.1.9 1akeA 1.5e-03 1zin 3.31.1.1.12 1shkA 2.5e-03 1shkA 3.31.1.2.1 2shkA 2.8e-03 1shkA 3.31.1.2.1 1zin 3.3e-05 1zin 3.31.1.1.14 There seems to be a pretty clear 3.31.1 hit, probably 3.31.1.1.6 Top-scoring alignments (among the three 3.31.1.1.6 2-way hits) are 3vtk/T0117-3vtk-global 3vtk 313 -74.15 -93.34 8.7e-41 1kimA/T0117-1kimA-local 1kimA 366 -98.58 -88.52 1.1e-38 1qhiA/T0117-1qhiA-local 1qhiA 366 -98.58 -88.52 1.1e-38 3vtk/T0117-3vtk-local 3vtk 343 -98.61 -88.51 1.1e-38 1kimA/T0117-1kimA-global 1kimA 300 -69.56 -87.01 4.9e-38 1qhiA/T0117-1qhiA-global 1qhiA 300 -69.56 -87.01 4.9e-38 1kimA/T0117-1kimA-vit 1kimA 366 -93.06 -86.76 6.3e-38 1qhiA/T0117-1qhiA-vit 1qhiA 366 -93.06 -86.76 6.3e-38 3vtk/T0117-3vtk-vit 3vtk 343 -93.12 -86.76 6.3e-38 1kimA/1kimA-T0117-global T0117 250 -41.20 -50.98 2.2e-22 1qhiA/1qhiA-T0117-global T0117 250 -40.11 -49.42 1.0e-21 3vtk/3vtk-T0117-global T0117 250 -40.83 -47.42 7.6e-21 1kimA/1kimA-T0117-local T0117 250 -50.88 -40.11 1.1e-17 3vtk/3vtk-T0117-local T0117 250 -51.71 -39.98 1.3e-17 1qhiA/1qhiA-T0117-local T0117 250 -50.50 -39.50 2.1e-17 1kimA/1kimA-T0117-vit T0117 250 -41.34 -37.89 1.1e-16 1qhiA/1qhiA-T0117-vit T0117 250 -39.93 -36.33 5.0e-16 3vtk/3vtk-T0117-vit T0117 250 -40.93 -36.24 5.5e-16 1qhiA/1qhiA-T0117-fssp-global T0117 250 -27.62 -31.60 5.7e-14 3vtk/T0117-3vtk-global should be same as 1qhiA/T0117-1qhiA-global in the area of interest, since templates are 100% identical over 298 residues, and structures only differ by 0.8 Angstroms Similarly for 1kimA and 1qhiA (100% id, 300 residues, 0.4 Angstroms). We should probably pick one of the dimer templates (1qhiA or 1kimA). We could align to one of of the other templates with the same sequence, if crystallization conditions seem more similar. Sat Aug 26 15:08:19 PDT 2000 Kevin Karplus Remade 2track predictions Top hits now % Sequence ID Length Simple Reverse E-value SCOP 5tmpA 213 -94.23 -72.19 1.8e-28 3.31.1.1.16 1kimA 366 -90.85 -70.88 1.4e-27 3.31.1.1.6 3vtk 343 -88.89 -69.20 3.7e-27 3.31.1.1.6 1qhiA 366 -89.99 -68.52 1.0e-26 3.31.1.1.6 2tmkA 216 -77.69 -53.33 3.3e-20 3.31.1.1.15 3tmkA 216 -76.73 -51.92 2.4e-19 3.31.1.1.15 1ukz 203 -68.96 -47.81 1.3e-17 3.31.1.1.2 5ukdA 194 -66.79 -44.57 2.7e-16 3.31.1.1.5 3adk 195 -63.50 -43.45 7.2e-16 3.31.1.1.7 3.31.1.1.6 still looks good, but we should also check out 3.31.1.1.16 and 3.31.1.1.15, though 5tmpA is a monomer and 3tmkA is an octomer. Tue Sep 5 10:35:23 PDT 2000 remaking 2track --- top hits unchanged. Wed Sep 6 12:27:14 PDT 2000 Kevin Karplus Top alignments (of 1qhiA, 3vtk, 1kimA, 5tmpA, 3tmkA) 3vtk/T0117-3vtk-global 3vtk 313 -74.15 -93.34 8.7e-41 mising three helices and strand from end of fold. 1kimA/T0117-1kimA-local 1kimA 366 -98.58 -88.52 1.1e-38 missing 4 helices and 2 strands from end of fold. 1qhiA/T0117-1qhiA-local 1qhiA 366 -98.58 -88.52 1.1e-38 missing 4 helices and 2 strands from end of fold. 3vtk/T0117-3vtk-local 3vtk 343 -98.61 -88.51 1.1e-38 1kimA/T0117-1kimA-global 1kimA 300 -69.56 -87.01 4.9e-38 1qhiA/T0117-1qhiA-global 1qhiA 300 -69.56 -87.01 4.9e-38 1kimA/T0117-1kimA-vit 1kimA 366 -93.06 -86.76 6.3e-38 1qhiA/T0117-1qhiA-vit 1qhiA 366 -93.06 -86.76 6.3e-38 3vtk/T0117-3vtk-vit 3vtk 343 -93.12 -86.76 6.3e-38 5tmpA/T0117-5tmpA-global 5tmpA 213 -69.25 -86.17 1.3e-37 Although the score is not as high as for 3vtk, I like this alignment better---ther's less missing. 1kimA/T0117-1kimA-local 1kimA 300 -92.05 -82.12 6.5e-36 1qhiA/T0117-1qhiA-local 1qhiA 300 -92.05 -82.12 6.5e-36 5tmpA/T0117-5tmpA-2track-global 5tmpA 213 -89.64 -80.62 5.4e-35 very similar to 5tmpA/T0117-5tmpA-global, but I like it's placement of gaps slightly better. 1kimA/T0117-1kimA-vit 1kimA 300 -86.31 -79.82 6.5e-35 1qhiA/T0117-1qhiA-vit 1qhiA 300 -86.31 -79.82 6.5e-35 5tmpA/T0117-5tmpA-2track-global 5tmpA 210 -89.46 -79.98 1.5e-34 1qhiA/T0117-1qhiA-2track-global 1qhiA 300 -71.49 -72.04 1.6e-31 5tmpA/T0117-5tmpA-2track-local 5tmpA 213 -94.23 -72.19 1.6e-31 1kimA/T0117-1kimA-2track-global 1kimA 300 -70.48 -71.61 4.4e-31 5tmpA/T0117-5tmpA-2track-local 5tmpA 210 -93.60 -71.57 4.4e-31 1kimA/T0117-1kimA-2track-local 1kimA 366 -90.85 -70.88 1.2e-30 3vtk/T0117-3vtk-2track-local 3vtk 343 -88.89 -69.20 3.2e-30 1kimA/T0117-1kimA-2track-global 1kimA 366 -57.42 -68.53 8.8e-30 1kimA/T0117-1kimA-2track-local 1kimA 300 -87.19 -68.13 8.8e-30 1qhiA/T0117-1qhiA-2track-local 1qhiA 366 -89.99 -68.52 8.8e-30 3vtk/T0117-3vtk-2track-global 3vtk 313 -70.19 -68.85 8.8e-30 1qhiA/T0117-1qhiA-2track-global 1qhiA 366 -57.02 -67.41 2.4e-29 3vtk/T0117-3vtk-2track-global 3vtk 343 -64.41 -67.83 2.4e-29 1qhiA/T0117-1qhiA-2track-local 1qhiA 300 -87.64 -66.96 6.5e-29 3vtk/T0117-3vtk-2track-local 3vtk 313 -87.25 -66.30 6.5e-29 3tmkA/T0117-3tmkA-global 3tmkA 216 -60.07 -63.39 1.3e-27 5tmpA/5tmpA-T0117-global T0117 250 -56.14 -58.37 1.9e-25 Also looks pretty good 3tmkA/3tmkA-T0117-global T0117 250 -50.27 -54.58 1.1e-23 1qhiA/1qhiA-T0117-fssp-global T0117 250 -27.62 -31.60 5.7e-14 3tmkA/3tmkA-T0117-fssp-global T0117 250 -27.07 -20.31 6.2e-09 3tmkA looks like ans "also-ran" let's forget it. I combined the best bits of 5tmpA alignment to create 5tmpA/T0117-5tmpA-karplus.a2m Let's submit it.