# List of top-scoring protein chains for t04-100-30-alpha-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 1u1wA 298 6.01e-03 1tm0A 350 9.24e-03 d.21.1.3 107147 1xubA 298 1.34e-02 1t6kA 278 2.57e-02 1ym5A 300 2.81e-02 2b3nA 159 6.36e-02 1o0pA 104 9.01e-02 d.58.7.1 86535 2gkeA 274 1.39e-01 1dp4A 435 1.41e-01 1dp4A c.93.1.1 35710 1j5pA 253 2.08e-01 d.81.1.3,c.2.1.3 71577,83092 1gqzA 274 2.21e-01 d.21.1.1,d.21.1.1 83311,83312 1w61A 414 2.73e-01 1p3dA 475 2.74e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1bwzA 274 9.53e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1wznA 252 9.60e-01 1yqfA 203 1.13e+00 1xtqA 177 1.19e+00 1rzhL 281 1.35e+00 f.26.1.1 98164 1sr8A 298 1.50e+00 e.54.1.1 105959 1t6aA 126 1.67e+00 d.129.8.1 106555 2azpA 318 1.73e+00 2cxcA 144 1.96e+00 1v7oA 165 2.12e+00 d.67.1.2 100480 1vdkA 466 2.18e+00 a.127.1.1 100561 1ycoA 279 2.42e+00 1gtzA 156 2.64e+00 c.23.13.1 70539 1d0iA 156 2.70e+00 2dhqA c.23.13.1 31383 1dkmA 410 3.08e+00 1dklA c.60.1.2 34000 1dkqA 410 3.15e+00 1dklA c.60.1.2 33998 1nnxA 109 3.22e+00 b.40.10.1 92013 1b56 135 3.25e+00 1hmt b.60.1.2 27183 2fr2A 172 3.32e+00 1zwxA 301 3.42e+00 1tzfA 259 3.70e+00 c.68.1.13 107476 1josA 128 3.80e+00 d.52.7.1 84191 1kkcA 221 4.10e+00 a.2.11.1,d.44.1.1 68660,68661 1oe4A 247 4.41e+00 c.18.1.3 86895 1tafB 70 4.64e+00 1tafB a.22.1.3 16482 1jc9A 269 4.96e+00 d.171.1.1 66490 4ubpC 570 5.32e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 2fs2A 151 5.97e+00 1sziA 247 6.37e+00 a.24.23.1 106159 1f3uA 118 6.79e+00 1f3uA b.65.1.1 27521 1ecfA 504 6.80e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1o17A 345 6.95e+00 a.46.2.1,c.27.1.1 80765,80766 1f06A 320 7.13e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 1ygs 234 7.54e+00 1ygs b.26.1.1 23907 1mxmA 254 8.15e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 2a1kA 233 8.16e+00 4uagA 437 8.36e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1qipA 183 8.51e+00 1qipA d.32.1.1 38470 2aioA 269 8.62e+00 1evhA 112 8.88e+00 1evhA b.55.1.4 26997 1nksA 194 8.99e+00 1nksA c.37.1.1 31886 1rzuA 485 8.99e+00 c.87.1.8 105140 1o70A 324 9.21e+00 b.118.1.1,b.118.1.1 81115,81116 1go4A 205 9.39e+00 d.135.1.1 70292 1x05A 129 9.40e+00 1wosA 364 9.47e+00 b.44.2.1,d.250.1.1 109468,109469 3proC 166 9.81e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1wycA 392 9.90e+00 1xttA 216 1.00e+01 1ush 550 1.07e+01 1ush d.114.1.1,d.159.1.2 40923,42079 2d93A 134 1.08e+01 1hp1A 516 1.09e+01 d.114.1.1,d.159.1.2 70976,70977 1jdrA 294 1.09e+01 1ryc a.93.1.1 62908 1ogsA 497 1.17e+01 b.71.1.2,c.1.8.3 86997,86998 1e1oA 504 1.18e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1wybA 392 1.18e+01 1smlA 269 1.23e+01 1smlA d.157.1.1 42053 1o20A 427 1.24e+01 c.82.1.1 86556 1wvcA 259 1.24e+01 1psuA 140 1.25e+01 d.38.1.5 88285 1zm0A 114 1.26e+01 1ixlA 131 1.28e+01 d.38.1.5 90717 1kk1A 410 1.29e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1qwnA 1045 1.37e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1vljA 407 1.42e+01 e.22.1.2 108832 1v4pA 157 1.46e+01 1ewqA 765 1.48e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1xx0A 127 1.48e+01 1gv3A 248 1.48e+01 a.2.11.1,d.44.1.1 70585,70586 1lj5A 379 1.48e+01 e.1.1.1 73928 1lylA 504 1.49e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1snzA 344 1.49e+01 b.30.5.4 98930 1ejxC 567 1.51e+01 b.92.1.1,c.1.9.2 83184,83185 1yc9A 442 1.51e+01 2f4nA 273 1.57e+01 2aneA 125 1.65e+01 1izmA 184 1.71e+01 a.199.1.1 90725 2a35A 215 1.73e+01 1qx4A 274 1.78e+01 b.43.4.2,c.25.1.1 104624,104625 1htyA 1015 1.80e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1dazC 99 1.80e+01 1hvc b.50.1.1 26501 1pfsA 78 1.84e+01 1pfsA b.40.4.7 25391 1a8rA 221 1.84e+01 1a8rA d.96.1.1 40587 1nscA 390 1.85e+01 2qwc b.68.1.1 27591 1wudA 89 1.85e+01 1z5hA 780 1.91e+01 1vm7A 311 1.91e+01 c.72.1.1 108884 2aliA 158 1.96e+01 1g5cA 170 1.97e+01 1g5cA c.53.2.1 60264 1jf9A 408 1.98e+01 1c0nA c.67.1.3 62931 1jb7A 495 1.99e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1u3wA 374 2.00e+01 1q15A 503 2.08e+01 c.26.2.1,d.153.1.1 95538,95539 1zbyA 294 2.08e+01 1on3A 523 2.08e+01 c.14.1.4,c.14.1.4 87107,87108 1y791 680 2.09e+01 1rsy 152 2.13e+01 1rsy b.7.1.2 23192 1uebA 184 2.14e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1r5eA 115 2.24e+01 1rl0A 255 2.24e+01 2fn0A 437 2.24e+01 1xizA 159 2.26e+01 1jcfA 344 2.26e+01 c.55.1.1,c.55.1.1 62878,62879 1h9dB 134 2.29e+01 2jhbA b.54.1.1 60822 1wekA 217 2.31e+01 1vl2A 421 2.34e+01 c.26.2.1,d.210.1.1 108708,108709 1kay 381 2.36e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1ab8A 220 2.51e+01 1azsA d.58.29.1 39414 1z53A 294 2.52e+01 1xjvA 294 2.63e+01 1z54A 132 2.65e+01 1iznB 277 2.66e+01 e.43.1.2 83848 2af4C 333 2.67e+01 1i1nA 226 2.67e+01 c.66.1.7 71102 1z94A 147 2.71e+01 1mkiA 330 2.71e+01 e.3.1.2 84994 2fkbA 180 2.74e+01 1sltA 134 2.74e+01 1c1lA b.29.1.3 24186 1t6cA 315 2.78e+01 c.55.1.8,c.55.1.8 106558,106559 1e94F 449 2.79e+01 1do0A c.37.1.20 32443 1ygaA 342 2.79e+01 1a7cA 379 2.80e+01 1sek e.1.1.1 42660 1zhhB 242 2.80e+01 1alu 186 2.82e+01 1alu a.26.1.1 16826 1umkA 275 2.82e+01 2bm3A 166 2.82e+01 1p7tA 731 2.82e+01 c.1.13.1 94319 1bupA 386 2.84e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2eutA 294 2.84e+01 2h0bA 184 2.88e+01 1fjgK 129 2.89e+01 1fjfK c.55.4.1 33733 1rybA 212 2.99e+01 c.56.3.1 98098 2d4qA 257 3.02e+01 1nbwA 607 3.02e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1ogdA 131 3.10e+01 c.133.1.1 92893 2a8yA 270 3.11e+01 1ecmA 109 3.12e+01 1ecmA a.130.1.1 19492 2fefA 294 3.14e+01 1h9sA 140 3.14e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1dykA 394 3.14e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1lp8A 254 3.17e+01 d.165.1.1 91082 1wab 232 3.19e+01 1wab c.23.10.3 31341 1jhjA 171 3.25e+01 b.18.1.9 66714 1uwkA 557 3.26e+01 e.51.1.1 108065 1xjcA 169 3.27e+01 1o97D 320 3.28e+01 c.26.2.3,c.31.1.2 81233,81234 2h4uA 145 3.35e+01 1avyA 74 3.38e+01 1avyB h.1.17.1 45656 2gjgA 248 3.41e+01 1wtaA 275 3.46e+01 2g1lA 104 3.51e+01 2cw8A 537 3.58e+01 2d0oA 610 3.60e+01 1vi6A 208 3.61e+01 c.23.15.1 100736 1nnsA 326 3.62e+01 c.88.1.1 85910 2bjbA 462 3.66e+01 1q5dA 419 3.68e+01 a.104.1.1 95891 1xipA 388 3.71e+01 1lox 662 3.74e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1otfA 62 3.81e+01 1otfA d.80.1.1 39820 1q87A 221 3.83e+01 e.47.1.1 96192 1kpf 126 3.85e+01 1kpf d.13.1.1 37507 1ku0A 388 3.92e+01 c.69.1.18 72994 1f08A 148 3.99e+01 1f08A d.89.1.2 59564 1oj6A 151 4.06e+01 a.1.1.2 93088 2etvA 346 4.10e+01 1n13B 113 4.10e+01 1ua4A 455 4.22e+01 c.72.1.3 99128 1rcy 151 4.23e+01 1rcy b.6.1.1 23018 1j3aA 142 4.25e+01 c.21.1.1 77070 1wthD 391 4.25e+01 1g5aA 628 4.28e+01 b.71.1.1,c.1.8.1 65152,65153 1ztdA 133 4.28e+01 1e5eA 404 4.29e+01 1ibjA c.67.1.3 59265 1kdgA 546 4.31e+01 c.3.1.2,d.16.1.1 77337,77338 1pj5A 830 4.34e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2fsrA 195 4.35e+01 1i7pA 274 4.41e+01 b.43.4.2,c.25.1.1 66048,66049 1ouwA 152 4.41e+01 b.77.3.1 93571 1i1iP 681 4.44e+01 1i1iP d.92.1.5 40297 1yuwA 554 4.44e+01 1sk4A 163 4.49e+01 d.118.1.1 105664 1hf8A 289 4.54e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2lhb 149 4.55e+01 2fal a.1.1.2 15597 1h0bA 256 4.60e+01 b.29.1.11 83422 1cjcA 460 4.60e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1kpeA 126 4.62e+01 1kpf d.13.1.1 37508 1vjrA 271 4.68e+01 c.108.1.14 100832 1s0uA 408 4.74e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1x8vA 455 4.74e+01 1d8cA 723 4.78e+01 1d8cA c.1.13.1 29325 1vh5A 148 4.81e+01 d.38.1.5 100642 1hdmB 193 4.83e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 1bvqA 141 4.92e+01 1bvqA d.38.1.1 38542 2bw8A 227 4.95e+01 1difA 99 4.96e+01 1fmb b.50.1.1 26503 1azsB 212 5.04e+01 1azsA d.58.29.1 39423 1pyoA 167 5.06e+01 c.17.1.1 95370 1qhtA 775 5.08e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1twuA 139 5.11e+01 d.32.1.8 107413 1mkrA 294 5.11e+01 a.93.1.1 84997 1qfgA 725 5.19e+01 1by5A f.4.3.3 43803 1v1qA 134 5.20e+01 1k8tA 510 5.24e+01 e.41.1.1 68316 1gzwA 134 5.25e+01 b.29.1.3 90535 1dgfA 497 5.27e+01 1cf9A e.5.1.1 42782 1qfhA 212 5.27e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 2dbbA 151 5.37e+01 1tkeA 224 5.43e+01 1yb3A 175 5.44e+01 1dtoA 221 5.46e+01 1dtoA b.91.1.1 28405 1lo7A 141 5.49e+01 d.38.1.1 74144 1x88A 359 5.53e+01 1q1rA 431 5.54e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1wq3A 322 5.54e+01 1xi3A 215 5.55e+01 c.1.3.1 109601 1qi7A 253 5.59e+01 1qi7A d.165.1.1 42210 1jniA 123 5.61e+01 a.138.1.3 71761 1y8tA 324 5.61e+01 1kv7A 488 5.63e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1gr0A 367 5.67e+01 c.2.1.3,d.81.1.3 70379,70380 1es9A 232 5.67e+01 1wab c.23.10.3 31340 1bebA 162 5.68e+01 1bebA b.60.1.1 27115 2b61A 377 5.69e+01 1ukkA 142 5.70e+01 d.227.1.1 99491 1spf 35 5.71e+01 1spf j.35.1.1 46254 1p5zB 263 5.76e+01 c.37.1.1 87815 1awd 94 5.79e+01 1awd d.15.4.1 37673 1hdfA 102 5.82e+01 1ag4 b.11.1.1 23627 1x8hA 228 5.84e+01 1bdo 80 5.91e+01 1bdo b.84.1.1 28214 1m7sA 484 5.95e+01 e.5.1.1 74574 1urvA 190 5.97e+01 1ut0A 190 5.97e+01 a.1.1.2 108012 1k82A 268 6.04e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1k8kE 178 6.05e+01 a.148.1.1 68311 2gfgA 193 6.07e+01 1q2yA 140 6.08e+01 d.108.1.1 95655 1od3A 168 6.09e+01 b.18.1.10 86825 1x8gA 227 6.10e+01 1e9lA 377 6.14e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1pzsA 208 6.20e+01 b.1.8.1 104397 1w8oA 601 6.23e+01 1w30A 201 6.23e+01 1f2rI 100 6.25e+01 1c9fA d.15.2.1 37641 1tdtA 259 6.27e+01 3tdt b.81.1.2 28055 2b59A 187 6.28e+01 1wocA 103 6.28e+01 1y1nA 291 6.31e+01 2fymA 431 6.38e+01 1vf8A 377 6.46e+01 1ue1A 164 6.48e+01 b.40.4.3 99243 1tt8A 164 6.52e+01 1eexA 554 6.53e+01 1dioA c.1.19.3 29650 1fw9A 164 6.53e+01 1fw9A d.190.1.1 60059 2yhx 457 6.55e+01 2yhx i.12.1.1 46024 1ash 150 6.58e+01 1ash a.1.1.2 15622 1by2 119 6.61e+01 1by2 d.170.1.1 42452 1gmiA 136 6.61e+01 b.7.1.1 65309 1fmtA 314 6.62e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1uj6A 227 6.70e+01 c.124.1.4,d.58.40.1 107898,107899 1e30A 155 6.74e+01 1rcy b.6.1.1 23016 2aifA 135 6.77e+01 2calA 154 6.77e+01 1nrjB 218 6.80e+01 c.37.1.8 86125 1uurA 473 6.82e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ig8A 486 6.88e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1kq3A 376 6.91e+01 e.22.1.2 68790 1ew2A 513 6.98e+01 1b8jA c.76.1.1 59525 1txvA 452 7.02e+01 1nxzA 246 7.02e+01 b.122.1.2,c.116.1.5 86391,86392 1e2wA 251 7.05e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 8acn 754 7.06e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1kr7A 110 7.07e+01 a.1.1.4 72890 1fezA 256 7.08e+01 1fezA c.108.1.3 43343 2f2hA 773 7.13e+01 2giyA 191 7.16e+01 1rm6A 769 7.17e+01 1m0dA 138 7.17e+01 c.52.1.17 74354 1vj7A 393 7.25e+01 a.211.1.1,d.218.1.8 100801,100802 1c96A 753 7.29e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1k66A 149 7.30e+01 c.23.1.1 90941 1txyA 104 7.40e+01 1pjxA 314 7.41e+01 b.68.6.1 104167 1e1aA 314 7.41e+01 1e1aA b.68.6.1 59155 1w6nA 134 7.42e+01 1fi8A 228 7.42e+01 5ptp b.47.1.2 26374 1dwkA 156 7.43e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1rreA 200 7.47e+01 d.14.1.10 97791 1q1fA 151 7.49e+01 a.1.1.2 104476 1srqA 341 7.51e+01 e.55.1.1 105967 1q3iA 214 7.54e+01 d.220.1.1 104524 1wcqA 601 7.58e+01 1v1pA 211 7.59e+01 b.40.2.2,d.15.6.1 108268,108269 2b30A 301 7.60e+01 2bx6A 350 7.62e+01 2bh9A 489 7.67e+01 1b8fA 509 7.77e+01 1b8fA a.127.1.2 19434 2blnA 305 7.77e+01 1wxxA 382 7.85e+01 1gt1A 159 7.85e+01 b.60.1.1 90515 2bvyA 475 7.86e+01 2a5vA 213 7.88e+01 1j1iA 296 8.02e+01 c.69.1.10 83977 1xe1A 116 8.03e+01 b.43.3.1 109571 1wmhB 86 8.05e+01 1o0wA 252 8.06e+01 a.149.1.1,d.50.1.1 80751,80752 1oohA 126 8.08e+01 a.39.2.1 93383 1jogA 146 8.14e+01 a.24.16.2 77142 2a19A 175 8.17e+01 1ualA 274 8.22e+01 c.116.1.4 88383 1ym0A 238 8.24e+01 1swvA 267 8.24e+01 1ykdA 398 8.33e+01 1i4uA 181 8.39e+01 b.60.1.1 61732 1odfA 290 8.43e+01 c.37.1.6 92782 1yg9A 330 8.47e+01 2go8A 122 8.48e+01 1jl0A 334 8.48e+01 1jenA d.156.1.1 63155 1q74A 303 8.56e+01 c.134.1.1 96019 1ryiA 382 8.58e+01 1fm4A 159 8.60e+01 1bv1 d.129.3.1 76186 1b06A 210 8.66e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1h2rL 534 8.67e+01 1h2rL e.18.1.1 43298 1m5yA 408 8.68e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1wuiL 534 8.77e+01 1iuhA 198 8.78e+01 d.61.1.2 83711 1gkmA 509 8.78e+01 a.127.1.2 70228 2av4A 162 8.79e+01 2bgkA 278 8.80e+01 1fcyA 236 8.88e+01 2lbd a.123.1.1 19282 1cl8A 276 8.89e+01 1ckqA c.52.1.1 33230 2bvbA 137 8.95e+01 2a74A 643 8.95e+01 1vlyA 338 8.96e+01 b.44.2.1,d.250.1.1 108871,108872