# List of top-scoring protein chains for t04-100-30-bys-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1xngA 268 9.82e-02 1tif 78 5.98e-01 1tif d.15.8.1 37836 1rsy 152 5.98e-01 1rsy b.7.1.2 23192 1f7dA 136 6.04e-01 1dun b.85.4.1 28353 1j83A 180 7.09e-01 b.18.1.12 66430 1dq3A 454 1.19e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1tyv 542 1.27e+00 1tyv b.80.1.6 28038 1wqsA 173 1.28e+00 2bu3A 254 1.29e+00 1r26A 125 1.34e+00 c.47.1.1 96847 1jmmA 377 1.41e+00 b.30.6.1 71749 1odkA 235 1.47e+00 c.56.2.1 86863 2a9mL 110 1.57e+00 1nkqA 259 1.57e+00 d.177.1.1 103862 1ekgA 127 1.68e+00 1dlxA d.82.2.1 40021 1pvyA 227 1.78e+00 d.115.1.2 95195 1ru4A 400 1.78e+00 b.80.1.9 97836 1yezA 68 1.87e+00 1lucB 324 2.00e+00 1lucA c.1.16.1 29548 1r8oA 96 2.09e+00 b.42.4.1 104852 1ub3A 220 2.13e+00 c.1.10.1 88395 1wzoA 246 2.15e+00 2gfaA 119 2.21e+00 1snnA 227 2.41e+00 d.115.1.2 105821 1qmeA 702 2.43e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1yu0A 381 2.50e+00 1gpmA 525 3.06e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1cqqA 180 3.10e+00 1cqqA b.47.1.4 26422 1jm1A 204 3.11e+00 b.33.1.1 71745 1gmyA 261 3.33e+00 d.3.1.1 76236 1zvhA 134 3.35e+00 1v8hA 107 3.71e+00 1j8mF 297 3.84e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1mhnA 59 3.98e+00 b.34.9.1 84964 1bb8 71 4.11e+00 2bb8 d.10.1.1 37478 1theA 260 4.32e+00 1theB d.3.1.1 37056 1j8yF 297 4.35e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1rzfL 213 4.43e+00 b.1.1.1,b.1.1.2 98152,98153 1svpA 161 4.49e+00 1svpA b.47.1.3 26384 1k3iA 656 4.50e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 2d13A 227 4.58e+00 1zvyA 136 4.82e+00 1p5hA 428 4.94e+00 c.123.1.1 87802 1el5A 389 5.04e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1eny 268 5.12e+00 1eny c.2.1.2 29910 1eo9A 209 5.16e+00 3pchA b.3.6.1 22731 1gof 639 5.29e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 2f9lA 199 5.46e+00 1obdA 306 5.47e+00 d.143.1.1 86767 1ok0A 74 5.55e+00 b.5.1.1 93191 2ak5A 64 5.58e+00 1nezG 128 5.63e+00 b.1.1.1 85592 1kv9A 668 5.74e+00 a.3.1.6,b.70.1.1 73056,73057 1j9bA 141 5.77e+00 c.47.1.12 66459 2gjgA 248 6.06e+00 1qtnA 164 6.13e+00 1pauA c.17.1.1 30999 1qmpA 130 6.14e+00 1dz3A c.23.1.1 31106 1mvfA 135 6.18e+00 b.1.1.1 85141 2a2pA 129 6.30e+00 1pguA 615 6.49e+00 b.69.4.1,b.69.4.1 88069,88070 1x0vA 354 6.51e+00 1yu2A 381 6.78e+00 1hoe 74 7.05e+00 1hoe b.5.1.1 22833 1uvzA 119 7.30e+00 1g0hA 252 7.32e+00 1dk4A e.7.1.1 60171 2g6fX 59 7.49e+00 1cb8A 678 7.65e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1bymA 97 7.70e+00 1bi0 b.34.1.2 24458 1k07A 263 7.72e+00 d.157.1.1 77218 1p5dX 463 7.92e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1tzyD 103 7.94e+00 a.22.1.1 107533 1xwyA 264 8.19e+00 1w85I 49 8.51e+00 1wu7A 434 8.66e+00 1idsA 207 8.73e+00 1avmA a.2.11.1,d.44.1.1 15722,38730 1zmaA 118 8.74e+00 1v6tA 255 8.83e+00 1vjgA 218 8.84e+00 c.23.10.6 100810 1nykA 165 8.86e+00 b.33.1.1 86408 1ut7A 171 8.94e+00 b.143.1.1 99906 1ebdC 41 8.96e+00 1ebdC a.9.1.1 16355 1vr0A 247 9.09e+00 3pcgA 200 9.09e+00 3pchA b.3.6.1 22647 1vckA 115 9.19e+00 1ru8A 232 9.23e+00 c.26.2.1 97849 1kx5B 102 9.39e+00 a.22.1.1 77594 1zkpA 268 9.42e+00 1yu4A 381 9.64e+00 1a48 306 9.68e+00 1a48 d.143.1.1 41590 1hq3D 103 9.91e+00 1aoiB a.22.1.1 16464 1o9wA 177 9.99e+00 b.2.3.5 86713 2cxaA 256 1.01e+01 1yu3A 381 1.02e+01 1sawA 225 1.03e+01 2a7yA 83 1.03e+01 2fomB 185 1.04e+01 1xfpA 142 1.04e+01 b.1.1.1 109587 1y96A 86 1.07e+01 1w4vA 119 1.07e+01 1jssA 224 1.08e+01 d.129.3.2 71844 1dz3A 130 1.11e+01 1dz3A c.23.1.1 31105 2g8yA 385 1.14e+01 1chmA 401 1.16e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1wy5A 317 1.17e+01 1tuaA 191 1.17e+01 d.51.1.1,d.51.1.1 107321,107322 1uwvA 433 1.18e+01 b.40.4.12,c.66.1.40 100128,100129 1ebfA 358 1.19e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1squA 155 1.20e+01 d.252.1.1 98971 1nkiA 135 1.22e+01 d.32.1.2 91941 1f89A 291 1.22e+01 d.160.1.1 64988 1vsd 152 1.22e+01 1cxqA c.55.3.2 33625 1v5vA 401 1.24e+01 2cokA 113 1.28e+01 2azwA 148 1.29e+01 1oivA 191 1.31e+01 c.37.1.8 93076 1jguH 217 1.32e+01 b.1.1.1,b.1.1.2 66688,66689 2dhqA 146 1.36e+01 2dhqA c.23.13.1 31382 1cxqA 162 1.37e+01 1cxqA c.55.3.2 33621 2gxfA 142 1.40e+01 1wmzA 140 1.40e+01 d.169.1.1 109422 1wdtA 665 1.41e+01 1yu1A 381 1.44e+01 1wlyA 333 1.46e+01 1oixA 191 1.46e+01 1m4vA 204 1.46e+01 b.40.2.2,d.15.6.1 74459,74460 1zk5A 176 1.52e+01 1j7lA 264 1.54e+01 d.144.1.6 62697 1qhoA 686 1.58e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1yc7A 124 1.59e+01 2as0A 396 1.65e+01 1s3cA 141 1.65e+01 1ee6A 197 1.65e+01 1ee6A b.80.1.1 28024 1wosA 364 1.66e+01 b.44.2.1,d.250.1.1 109468,109469 2aq8A 269 1.67e+01 1pbe 394 1.70e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1i7oA 429 1.70e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1lv7A 257 1.74e+01 c.37.1.20 78232 1snyA 267 1.80e+01 c.2.1.2 105833 1kb0A 677 1.81e+01 a.3.1.6,b.70.1.1 68378,68379 1zczA 464 1.87e+01 1bqhG 129 1.87e+01 1cd8 b.1.1.1 19715 1gttA 429 1.88e+01 d.177.1.1,d.177.1.1 70529,70530 1k0iA 394 1.99e+01 c.3.1.2,d.16.1.2 67942,67943 1nycA 111 2.00e+01 b.61.2.2 92336 1tp6A 128 2.01e+01 d.17.4.12 107184 1jj2S 119 2.01e+01 1ffkQ b.34.5.1 63104 1s72T 120 2.02e+01 b.34.5.1 105339 1eudB 396 2.03e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1lba 146 2.04e+01 1lba d.118.1.1 41062 1xer 103 2.05e+01 1xer d.58.1.3 38990 1bjmA 216 2.06e+01 8fabA b.1.1.1,b.1.1.2 20524,21460 2g6bA 180 2.08e+01 1l1jA 239 2.08e+01 b.47.1.1 84516 1cojA 212 2.09e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1uv4A 293 2.10e+01 1yioA 208 2.11e+01 1vdwA 254 2.11e+01 e.7.1.1 100569 1lqpA 135 2.11e+01 d.32.1.2 78151 1f5aA 513 2.11e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1w44A 331 2.11e+01 1x99A 145 2.12e+01 1ni5A 433 2.13e+01 c.26.2.5,d.229.1.1 80533,80534 1xcbA 211 2.16e+01 a.4.5.38,c.2.1.12 109552,109553 1k2yX 463 2.18e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1yoxA 250 2.19e+01 1qzzA 374 2.25e+01 a.4.5.29,c.66.1.12 96719,96720 2fp7B 172 2.27e+01 1gxuA 91 2.29e+01 d.58.10.1 76378 1o6sB 105 2.30e+01 b.1.6.1 81096 2fimA 276 2.31e+01 1wr8A 231 2.32e+01 1ykjA 394 2.33e+01 2pvbA 107 2.35e+01 1a75A a.39.1.4 17205 1i8nA 126 2.37e+01 1i8nA g.10.1.2 61976 1s98A 107 2.44e+01 b.124.1.1 105377 1t6t1 118 2.44e+01 1yllA 200 2.45e+01 1kcfA 258 2.46e+01 a.140.2.1,c.55.3.7 68434,68435 1erw 105 2.54e+01 1erv c.47.1.1 32745 1c8zA 265 2.60e+01 1c8zA d.23.1.1 38375 1vfgA 390 2.64e+01 a.173.1.1,d.218.1.4 108570,108571 1aiu 105 2.71e+01 1erv c.47.1.1 32746 1vqoT 120 2.73e+01 1faeA 629 2.75e+01 1fce a.102.1.2 18837 1fe0A 68 2.76e+01 1cc8A d.58.17.1 39345 1mxmA 254 2.77e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1f06A 320 2.79e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1zrjA 50 2.81e+01 1erv 105 2.82e+01 1erv c.47.1.1 32743 1snzA 344 2.87e+01 b.30.5.4 98930 1mqkH 127 2.89e+01 b.1.1.1 85053 2bl0C 142 2.89e+01 1jbeA 128 2.91e+01 3chy c.23.1.1 62845 2f5gA 133 2.91e+01 1kskA 234 2.94e+01 d.66.1.5,d.265.1.3 72920,90389 1r6vA 671 2.96e+01 1x8dA 104 2.96e+01 1fdr 248 2.98e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2fp4B 395 2.99e+01 1ojaA 520 3.02e+01 c.3.1.2,d.16.1.5 93096,93097 2b59A 187 3.02e+01 1po5A 476 3.03e+01 a.104.1.1 94963 1p0zA 131 3.03e+01 d.110.6.1 93882 1fnc 314 3.07e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1ars 396 3.09e+01 1ajsA c.67.1.1 34287 1d1qA 161 3.10e+01 1dg9A c.44.1.1 32642 2fyxA 143 3.12e+01 1y9wA 140 3.14e+01 1rz4A 226 3.15e+01 a.4.5.53,a.118.1.18 105131,105132 1drw 273 3.16e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1s3eA 520 3.21e+01 c.3.1.2,d.16.1.5 98426,98427 1fmtA 314 3.24e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2bo9A 308 3.31e+01 1i2aA 219 3.32e+01 e.24.1.1 90660 1iq4A 179 3.32e+01 1iq4A d.77.1.1 62641 1o4sA 389 3.34e+01 c.67.1.1 86620 1tjyA 316 3.42e+01 c.93.1.1 107062 1qr0A 228 3.43e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1jidA 128 3.46e+01 d.201.1.1 66735 1ahxA 396 3.47e+01 1ajsA c.67.1.1 34293 1s1qA 145 3.50e+01 d.20.1.2 98351 1dceB 331 3.51e+01 1dceB a.102.4.3 18872 1qisA 396 3.51e+01 1ajsA c.67.1.1 34284 2a7mA 250 3.51e+01 1t2jA 116 3.51e+01 1wznA 252 3.52e+01 1x0pA 143 3.53e+01 1rwiA 270 3.58e+01 b.68.9.1 97987 1wd7A 261 3.60e+01 1g9gA 629 3.60e+01 a.102.1.2 83279 1m6iA 493 3.60e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1viaA 175 3.62e+01 c.37.1.2 100754 1xv2A 237 3.63e+01 1g5cA 170 3.64e+01 1g5cA c.53.2.1 60264 1souA 194 3.66e+01 c.124.1.6 105858 1rkqA 282 3.66e+01 c.108.1.10 97621 1qmyA 167 3.69e+01 1qmyA d.3.1.2 37094 1fnd 314 3.71e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 2fw2A 260 3.74e+01 1f7sA 139 3.77e+01 1cof d.109.1.2 40857 2a5yB 549 3.78e+01 1nfp 228 3.82e+01 1nfp c.1.16.2 29555 1qipA 183 3.83e+01 1qipA d.32.1.1 38470 1rifA 282 3.83e+01 c.37.1.23 97507 1nciA 110 3.84e+01 1edhA b.1.6.1 22191 1ml9A 302 3.85e+01 b.85.7.1 79282 1gzsB 165 3.90e+01 a.168.1.1 76425 1ermA 263 3.92e+01 1btl e.3.1.1 42690 1i8kB 124 3.94e+01 b.1.1.1 71131 1wdcB 156 3.98e+01 1wdcB a.39.1.5 17302 1ek0A 170 3.99e+01 1ctqA c.37.1.8 32076 1q79A 514 4.02e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1zcoA 262 4.04e+01 1qy6A 274 4.06e+01 b.47.1.1 96574 1lcyA 325 4.11e+01 b.36.1.4,b.47.1.1 73834,73835 1mq7A 154 4.15e+01 b.85.4.1 79404 1uuzA 137 4.19e+01 d.233.1.1 100024 1skoA 143 4.22e+01 d.110.7.1 105676 1lfo 128 4.22e+01 1hmt b.60.1.2 27223 1bx1A 314 4.24e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1uz8B 212 4.28e+01 b.1.1.1,b.1.1.2 108168,108169 1o4wA 147 4.37e+01 c.120.1.1 86629 1tjgH 237 4.43e+01 1dgwA 178 4.44e+01 1dgwA b.82.1.2 28090 2cpgA 45 4.45e+01 2cpgA a.43.1.3 17455 1kk8B 139 4.46e+01 a.39.1.5 77430 1fvuB 125 4.46e+01 1ixxB d.169.1.1 42346 1u0tA 307 4.50e+01 e.52.1.1 107567 1u24A 337 4.54e+01 1jb9A 316 4.61e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1knmA 130 4.64e+01 b.42.2.1 72781 1v5xA 203 4.64e+01 c.1.2.4 100377 1g0sA 209 4.69e+01 1g0sA d.113.1.1 60187 1ve1A 304 4.75e+01 1dcfA 136 4.75e+01 1dcfA c.23.1.2 31124 1v74B 87 4.77e+01 a.24.20.1 100443 1ihjA 98 4.82e+01 1pdr b.36.1.1 62382 2axcA 264 4.85e+01 1ax4A 467 4.88e+01 1ax4A c.67.1.2 34391 1ugpB 226 4.90e+01 b.34.4.4 107832 1hyxH 224 5.02e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 2bcmA 165 5.06e+01 1r94A 118 5.06e+01 b.124.1.1 97251 1luzA 88 5.08e+01 b.40.4.5 74271 1rcwA 231 5.11e+01 a.132.1.4 97299 2ebn 289 5.13e+01 2ebn c.1.8.5 28990 2b4rO 345 5.14e+01 1gyhA 318 5.17e+01 b.67.2.1 70757 1xauA 122 5.17e+01 1iu1A 146 5.21e+01 b.1.10.2 71428 2g9iA 249 5.25e+01 1mk0A 97 5.25e+01 d.226.1.1 79216 2a5jA 191 5.28e+01 2absA 383 5.30e+01 2ffcA 353 5.32e+01 1upaA 573 5.34e+01 c.31.1.3,c.36.1.5,c.36.1.9 99714,99715,99716 1sixA 174 5.35e+01 b.85.4.1 98892 1ko7A 314 5.35e+01 c.98.2.1,c.91.1.2 72797,72798 1xs1A 193 5.38e+01 1l0lA 446 5.50e+01 d.185.1.1,d.185.1.1 84482,84483 1whzA 70 5.51e+01 1erzA 303 5.51e+01 1erzA d.160.1.2 59498 1vrbA 342 5.52e+01 2ew2A 316 5.54e+01 1xnkA 196 5.58e+01 8fabA 212 5.60e+01 8fabA b.1.1.1,b.1.1.2 19772,20882 1vphA 149 5.62e+01 2ga9D 469 5.64e+01 1fw9A 164 5.65e+01 1fw9A d.190.1.1 60059 1f8gA 384 5.66e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1ol0A 121 5.67e+01 b.1.1.1 93296 1yn9A 169 5.67e+01 2bkkA 264 5.69e+01 1ra0A 430 5.71e+01 1vhsA 175 5.71e+01 d.108.1.1 100698 1k6wA 426 5.71e+01 b.92.1.2,c.1.9.5 68236,68237 1uohA 226 5.71e+01 d.211.1.1 99690 1vrmA 325 5.72e+01 1hlvA 131 5.76e+01 a.4.1.7,a.4.1.7 65854,65855 1kl9A 182 5.78e+01 b.40.4.5 72681 1w6sA 599 5.79e+01 1yg9A 330 5.81e+01 1b5fB 87 5.84e+01 1b5fB 1f1eA 154 5.84e+01 a.22.1.2 64927 2bm3A 166 5.88e+01 1h1aA 191 5.94e+01 b.29.1.11 83450 1jyoA 130 5.97e+01 d.198.1.1 67483 1mvwB 145 6.00e+01 i.15.1.1 79524 1l6rA 227 6.07e+01 c.108.1.10 77768 1vlmA 219 6.07e+01 c.66.1.41 108836 1pmzA 86 6.17e+01 a.39.1.10 104195 1uf5A 303 6.17e+01 d.160.1.2 107808 1dy9A 187 6.20e+01 1jxpA b.47.1.3 26400 1x88A 359 6.25e+01 2agcA 162 6.30e+01 1yhtA 367 6.34e+01 1liiA 363 6.39e+01 c.72.1.1 73921 1gqiA 708 6.40e+01 c.1.8.10,d.92.2.2 76279,76280 1btl 263 6.41e+01 1btl e.3.1.1 42691 1faaA 124 6.42e+01 1erv c.47.1.1 32738 1tt8A 164 6.44e+01 1ppjA 446 6.47e+01 d.185.1.1,d.185.1.1 104252,104253 1ww7A 160 6.49e+01 1tafB 70 6.53e+01 1tafB a.22.1.3 16482 1qznA 173 6.55e+01 b.2.2.2 104669 1hhsA 664 6.58e+01 1hi0P 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