# List of top-scoring protein chains for t06-100-30-str2-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 1ockA 412 1.73e-01 c.117.1.1 86802 1dyqA 234 2.88e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2aioA 269 3.13e-01 1m93A 55 8.18e-01 e.1.1.1 91235 2bg5A 324 9.71e-01 1a53 247 1.25e+00 1a53 c.1.2.4 28564 1yiyA 429 1.77e+00 1iz5A 249 1.86e+00 d.131.1.2,d.131.1.2 83834,83835 2d1uA 104 2.10e+00 1fl2A 310 2.61e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 2fvtA 135 2.76e+00 1sqsA 242 2.77e+00 c.23.5.5 98968 1vfsA 386 2.85e+00 b.49.2.2,c.1.6.1 108584,108585 1qi9A 556 2.91e+00 1qhbA a.111.1.2 19053 1repC 251 3.45e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1qhlA 227 3.94e+00 1qhlA c.37.1.12 32382 1sr4B 261 4.32e+00 d.151.1.1 105949 1eceA 358 4.45e+00 1eceA c.1.8.3 28813 1e4mM 501 4.78e+00 1e70M c.1.8.4 59226 2a2pA 129 5.05e+00 2aefA 234 5.09e+00 2fclA 169 5.25e+00 1fhgA 154 5.71e+00 1tlk b.1.1.4 21706 2rslA 140 5.90e+00 2rslA c.53.1.1 33345 1xn5A 146 6.05e+00 1v0lA 313 6.45e+00 c.1.8.3 108207 1rwiA 270 6.49e+00 b.68.9.1 97987 1q59A 172 6.65e+00 f.1.4.1 95881 2g9iA 249 7.05e+00 1g8lA 411 7.13e+00 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1of8A 370 7.33e+00 c.1.10.4 92819 1jhfA 202 7.43e+00 a.4.5.2,b.87.1.1 63057,63058 1ma3A 253 7.48e+00 c.31.1.5 78883 1hqz1 141 7.48e+00 1y96B 85 7.69e+00 1k38A 254 7.87e+00 e.3.1.1 84303 1h72C 296 7.98e+00 d.14.1.5,d.58.26.1 60712,60713 1t9bA 677 8.14e+00 1xfcA 384 8.21e+00 1hdoA 206 8.40e+00 1he2A c.2.1.2 60965 1xewY 172 8.45e+00 1wmhA 89 8.85e+00 1my6A 199 9.24e+00 a.2.11.1,d.44.1.1 85232,85233 2dfkA 402 9.24e+00 1c7qA 445 9.79e+00 2pgi c.80.1.2 35307 1vr0A 247 9.84e+00 1wouA 123 1.06e+01 c.47.1.16 109471 1ej0A 180 1.12e+01 1ej0A c.66.1.2 34179 2d1pA 140 1.13e+01 1o58A 303 1.18e+01 c.79.1.1 92491 1o1zA 234 1.22e+01 c.1.18.3 86555 1bia 321 1.24e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2fgtA 417 1.25e+01 1vc4A 254 1.26e+01 c.1.2.4 100557 2a15A 139 1.27e+01 2amhA 207 1.27e+01 1e9rA 437 1.29e+01 c.37.1.11 64827 2culA 232 1.29e+01 1tt8A 164 1.30e+01 1woqA 267 1.31e+01 c.55.1.10,c.55.1.10 109462,109463 2f4mA 295 1.33e+01 1nijA 318 1.33e+01 c.37.1.10,d.237.1.1 85741,85742 1ft5A 211 1.34e+01 1bvb a.138.1.3 19681 1wcdJ 441 1.38e+01 1ur1A 378 1.44e+01 c.1.8.3 99804 1xkrA 206 1.47e+01 1yizA 429 1.55e+01 2cygA 312 1.57e+01 1pyfA 312 1.61e+01 c.1.7.1 95334 1d2oA 187 1.61e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1mkaA 171 1.62e+01 1mkaA d.38.1.2 38543 1c52 131 1.62e+01 1c52 a.3.1.1 15810 1wrjA 156 1.62e+01 1lqtA 456 1.66e+01 c.3.1.1,c.4.1.1 74198,74199 1xcbA 211 1.73e+01 a.4.5.38,c.2.1.12 109552,109553 2bbkL 125 1.75e+01 2bbkL g.21.1.1 44882 1toaA 313 1.78e+01 1toaA c.92.2.2 35598 1wmhB 86 1.82e+01 1regX 122 1.87e+01 1regX d.58.27.1 39406 1n8kA 374 1.90e+01 b.35.1.2,c.2.1.1 80298,80299 2b7eA 59 1.91e+01 1u9cA 224 1.93e+01 1bdfA 235 1.94e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1vr7A 142 1.95e+01 2awpA 198 1.97e+01 1sek 378 1.99e+01 1sek e.1.1.1 42675 2afbA 351 1.99e+01 2bo4A 397 2.03e+01 1gwmA 153 2.04e+01 b.18.1.19 83348 1nf3C 128 2.06e+01 b.36.1.1 85596 1wlyA 333 2.12e+01 2gmqA 118 2.13e+01 2cxcA 144 2.16e+01 1quqB 121 2.19e+01 1quqB b.40.4.3 25305 1v30A 124 2.23e+01 1s55A 156 2.30e+01 1tr9A 341 2.34e+01 1vicA 262 2.40e+01 c.68.1.13 100756 1fg7A 356 2.44e+01 1gewA c.67.1.1 59819 1bby 69 2.48e+01 2bby a.4.5.15 16149 1zthA 258 2.50e+01 1vjpA 394 2.53e+01 c.2.1.3,d.81.1.3 100828,100829 1id0A 152 2.53e+01 d.122.1.3 66111 1rh9A 373 2.58e+01 1pbjA 125 2.58e+01 d.37.1.1,d.37.1.1 94414,94415 2axpA 173 2.58e+01 1xubA 298 2.58e+01 1b25A 619 2.62e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1ddf 127 2.63e+01 1ddf a.77.1.2 18423 1m4jA 142 2.63e+01 d.109.1.2 78602 1vddA 228 2.67e+01 e.49.1.1 108519 2axwA 134 2.68e+01 1wb4A 297 2.68e+01 1ri5A 298 2.70e+01 c.66.1.34 97502 1dljA 402 2.76e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1uekA 275 2.81e+01 d.14.1.5,d.58.26.5 88483,88484 1r6jA 82 2.84e+01 b.36.1.1 97151 1e0tA 470 2.86e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1kwiA 101 2.86e+01 d.17.1.3 77564 1uc7A 125 2.97e+01 c.47.1.1 99163 1o98A 511 2.99e+01 c.105.1.1,c.76.1.3 86684,86685 1azo 232 3.03e+01 1azo c.52.1.14 33329 1flcA 432 3.09e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1ve6A 582 3.12e+01 1fzqA 181 3.17e+01 1hurA c.37.1.8 32060 1h7zA 194 3.20e+01 1qhvA b.21.1.1 60733 1vcvA 226 3.24e+01 1o9gA 250 3.29e+01 c.66.1.29 86692 1vhxA 150 3.32e+01 c.55.3.8 100712 1f9vA 347 3.38e+01 1bg2 c.37.1.9 59745 1zhrA 238 3.41e+01 2g0uA 92 3.46e+01 1juvA 193 3.50e+01 c.71.1.1 90912 1o0yA 260 3.53e+01 c.1.10.1 80756 1omzA 293 3.56e+01 c.68.1.15 87093 1nwwA 149 3.58e+01 d.17.4.8 86306 1kqpA 271 3.60e+01 c.26.2.1 72883 2gh1A 301 3.61e+01 2fj6A 82 3.65e+01 1xedA 117 3.65e+01 1d1gA 168 3.66e+01 1d1gA c.71.1.1 34889 1t64A 377 3.67e+01 c.42.1.2 106543 1h2cA 140 3.67e+01 b.31.1.1 83462 2g5dA 422 3.68e+01 1rwzA 245 3.75e+01 d.131.1.2,d.131.1.2 98005,98006 1uwzA 136 3.77e+01 c.97.1.1 108081 1fr3A 67 3.79e+01 1fr3A b.40.6.1 25436 1luzA 88 3.83e+01 b.40.4.5 74271 1mo9A 523 3.83e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1c7nA 399 3.84e+01 1d2fA c.67.1.3 34413 1ob8A 135 3.86e+01 1qo2A 241 3.86e+01 1qo2A c.1.2.1 28533 1jlyA 304 3.94e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 2fh7A 595 3.95e+01 1s50A 259 4.03e+01 1ny4A 82 4.04e+01 b.40.4.5 92316 1udc 338 4.06e+01 1xel c.2.1.2 29785 1cq3A 233 4.07e+01 1cq3A b.27.1.1 23923 1ri6A 343 4.07e+01 b.69.11.1 97503 1xvqA 175 4.12e+01 1un7A 400 4.14e+01 b.92.1.5,c.1.9.10 99657,99658 1duvG 333 4.14e+01 1othA c.78.1.1,c.78.1.1 35228,35229 2d9rA 104 4.15e+01 1uheA 97 4.15e+01 1mixA 206 4.20e+01 a.11.2.1,b.55.1.5 79166,79167 1nq6A 302 4.20e+01 c.1.8.3 92046 1i8fA 81 4.25e+01 1i8fA b.38.1.1 61959 1l5oA 356 4.28e+01 c.39.1.1 77711 1p5vA 235 4.33e+01 b.1.11.1,b.7.2.1 87812,87813 1wyxA 69 4.35e+01 1wluA 136 4.42e+01 1qwnA 1045 4.51e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1m7vA 363 4.53e+01 d.174.1.1 78748 1xttA 216 4.56e+01 1bn8A 420 4.56e+01 1pcl b.80.1.1 28022 1z52A 470 4.63e+01 2hvm 273 4.63e+01 1cnv c.1.8.5 28985 1x6mA 196 4.65e+01 1y9aA 360 4.66e+01 1ll2A 333 4.70e+01 c.68.1.14 74005 2aq4A 434 4.80e+01 1ta3B 303 4.85e+01 c.1.8.3 106732 1w7lA 422 4.87e+01 c.67.1.1 109226 1no5A 114 4.89e+01 d.218.1.5 92014 1rf6A 427 4.90e+01 d.68.2.2 97366 1thg 544 4.93e+01 1thg c.69.1.17 34763 1k77A 260 4.94e+01 c.1.15.5 72096 2a9dA 372 4.95e+01 1bg6 359 5.00e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 2ewcA 126 5.00e+01 1y1oA 203 5.06e+01 1oa2A 218 5.10e+01 b.29.1.11 86721 1tiqA 180 5.10e+01 d.108.1.1 107010 1u46A 291 5.10e+01 d.144.1.7 107656 1s6lA 212 5.10e+01 2gfgA 193 5.11e+01 1wu3I 161 5.13e+01 1qlmA 316 5.16e+01 1qlmA d.147.1.1 41765 1j1yA 136 5.16e+01 d.38.1.5 90776 1vr4A 103 5.22e+01 1jy1A 464 5.22e+01 d.136.1.3,d.136.1.3 67438,67439 1gd1O 334 5.27e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2c7hA 86 5.40e+01 1ysjA 404 5.43e+01 1yzxA 226 5.48e+01 1sn4A 64 5.54e+01 1aho g.3.7.1 44136 1p42A 270 5.54e+01 d.14.1.7,d.14.1.7 87754,87755 1g60A 260 5.62e+01 c.66.1.11 70151 1k0fA 277 5.64e+01 c.92.2.2 71974 1wspA 84 5.66e+01 1exg 110 5.69e+01 1exg b.2.2.1 22387 1rsy 152 5.70e+01 1rsy b.7.1.2 23192 1qlwA 328 5.76e+01 1qlwA c.69.1.15 34722 1rfeA 162 5.82e+01 1jjzA 29 5.82e+01 g.3.3.1 71699 1qhvA 195 5.84e+01 1qhvA b.21.1.1 23842 1u3wA 374 5.84e+01 1zp4A 304 5.86e+01 1x74A 360 5.93e+01 2ptd 298 5.99e+01 2plc c.1.18.2 29605 2bl9A 238 6.03e+01 1w9zA 283 6.04e+01 1k7hA 476 6.06e+01 c.76.1.1 72101 1cby 259 6.08e+01 1cby d.103.1.1 40705 1g6gA 127 6.11e+01 1g6gA b.26.1.2 23916 2czrA 226 6.14e+01 1gqzA 274 6.15e+01 d.21.1.1,d.21.1.1 83311,83312 1vkuA 100 6.17e+01 a.28.1.1 108690 1r7aA 504 6.19e+01 b.71.1.1,c.1.8.1 97192,97193 1a8q 274 6.25e+01 1brt c.69.1.12 34702 1ylqA 96 6.28e+01 1ggzA 148 6.34e+01 a.39.1.5 70176 2aqjA 538 6.42e+01 1ns5A 155 6.54e+01 c.116.1.3 80705 1ok7A 366 6.55e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1yc5A 246 6.57e+01 1wqaA 455 6.58e+01 1xyiA 66 6.61e+01 2g50A 530 6.62e+01 1hm9A 468 6.64e+01 b.81.1.4,c.68.1.5 65866,65867 1yg6A 193 6.69e+01 1yy7A 213 6.70e+01 1ydmA 187 6.70e+01 1o57A 291 6.74e+01 a.4.5.40,c.61.1.1 92483,92484 2akoA 251 6.78e+01 1vqoI 162 6.83e+01 1ep3B 262 6.86e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1g66A 207 6.90e+01 1bs9 c.69.1.30 31329 1ecfA 504 6.91e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1vetA 124 6.94e+01 d.110.7.1 108553 1ex0A 731 6.94e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1zc1A 208 6.99e+01 1kblA 873 7.15e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1tuoA 464 7.22e+01 2gzqA 200 7.26e+01 2asbA 251 7.32e+01 2b3wA 168 7.38e+01 1u6tA 121 7.38e+01 1vbuA 328 7.40e+01 2c0nA 203 7.49e+01 1enwA 114 7.50e+01 1enwA a.5.4.1 16291 1jer 138 7.52e+01 2cbp b.6.1.1 23022 2trxA 108 7.54e+01 1thx c.47.1.1 32719 1s4iA 175 7.58e+01 1w2iA 91 7.58e+01 d.58.10.1 109127 2gw6A 123 7.58e+01 1yaxA 153 7.66e+01 1vbvA 105 7.68e+01 1xsqA 168 7.71e+01 1t0aA 159 7.72e+01 2fug1 438 7.76e+01 1zruA 264 7.93e+01 1qg8A 255 7.96e+01 1qg8A c.68.1.1 34505 5nul 138 7.98e+01 5nul c.23.5.1 31191 1zhvA 134 8.03e+01 2a1fA 247 8.03e+01 1t0hA 132 8.03e+01 b.34.2.1 106207 2bwfA 77 8.06e+01 1r5tA 142 8.07e+01 c.97.1.1 104812 1et9A 204 8.07e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1zpsA 138 8.09e+01 1fp1D 372 8.10e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 2bynA 227 8.11e+01 1ztsA 139 8.13e+01 1k7jA 206 8.14e+01 d.115.1.1 72103 1wwhA 119 8.17e+01 1b6g 310 8.25e+01 1b6g c.69.1.8 34661 1ve0A 134 8.28e+01 2fkcA 247 8.31e+01 1s5dA 240 8.31e+01 d.166.1.1 98541 1nu4A 97 8.31e+01 d.58.7.1 80731 1xtoA 311 8.33e+01 1bg4 302 8.36e+01 1taxA c.1.8.3 28806 2akaB 299 8.42e+01 2etxA 209 8.44e+01 1ydyA 356 8.47e+01 1j0dA 341 8.53e+01 c.79.1.1 83902 1g291 372 8.56e+01 1g291 1gutA 68 8.60e+01 b.40.6.1 65576 1h09A 338 8.62e+01 b.109.1.1,c.1.8.8 83420,83421 1n7eA 97 8.80e+01 b.36.1.1 91691 1oj4A 283 8.80e+01 d.14.1.5,d.58.26.5 93083,93084 1cojA 212 8.85e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1h9mA 145 8.89e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1whbA 157 8.97e+01 2cx5A 158 8.97e+01 1e9gA 286 8.98e+01 1wgjA b.40.5.1 59393