# 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 4.71e-03 1tm0A 350 8.88e-03 d.21.1.3 107147 1xubA 298 1.01e-02 1t6kA 278 1.76e-02 1ym5A 300 3.53e-02 2b3nA 159 5.23e-02 1o0pA 104 6.16e-02 d.58.7.1 86535 2gkeA 274 1.61e-01 1j5pA 253 2.04e-01 d.81.1.3,c.2.1.3 71577,83092 1dp4A 435 2.15e-01 1dp4A c.93.1.1 35710 1p3dA 475 2.24e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gqzA 274 2.28e-01 d.21.1.1,d.21.1.1 83311,83312 1w61A 414 3.27e-01 1yqfA 203 9.10e-01 2azpA 318 9.56e-01 1wznA 252 1.07e+00 1rzhL 281 1.08e+00 f.26.1.1 98164 1bwzA 274 1.17e+00 1bwzA d.21.1.1,d.21.1.1 38337,38338 1sr8A 298 1.38e+00 e.54.1.1 105959 1t6aA 126 1.69e+00 d.129.8.1 106555 1v7oA 165 1.72e+00 d.67.1.2 100480 2cxcA 144 1.77e+00 1vdkA 466 2.22e+00 a.127.1.1 100561 1gtzA 156 2.22e+00 c.23.13.1 70539 1ycoA 279 2.24e+00 1d0iA 156 2.25e+00 2dhqA c.23.13.1 31383 1xtqA 177 2.53e+00 1nnxA 109 2.58e+00 b.40.10.1 92013 2fr2A 172 2.73e+00 1kkcA 221 3.15e+00 a.2.11.1,d.44.1.1 68660,68661 1dkmA 410 3.40e+00 1dklA c.60.1.2 34000 1jc9A 269 3.40e+00 d.171.1.1 66490 1dkqA 410 3.45e+00 1dklA c.60.1.2 33998 1tzfA 259 3.88e+00 c.68.1.13 107476 1tafB 70 4.11e+00 1tafB a.22.1.3 16482 1b56 135 4.21e+00 1hmt b.60.1.2 27183 2fs2A 151 4.26e+00 4ubpC 570 4.76e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 1hp1A 516 4.91e+00 d.114.1.1,d.159.1.2 70976,70977 1ygs 234 4.94e+00 1ygs b.26.1.1 23907 1ush 550 5.01e+00 1ush d.114.1.1,d.159.1.2 40923,42079 1oe4A 247 5.07e+00 c.18.1.3 86895 1josA 128 5.79e+00 d.52.7.1 84191 1f3uA 118 5.80e+00 1f3uA b.65.1.1 27521 1go4A 205 5.99e+00 d.135.1.1 70292 1xttA 216 6.34e+00 1ecfA 504 6.41e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1mxmA 254 6.48e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1kk1A 410 6.83e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1sziA 247 6.92e+00 a.24.23.1 106159 1evhA 112 7.10e+00 1evhA b.55.1.4 26997 1zwxA 301 7.50e+00 1o70A 324 7.67e+00 b.118.1.1,b.118.1.1 81115,81116 4uagA 437 7.74e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 2a1kA 233 9.27e+00 1nksA 194 9.48e+00 1nksA c.37.1.1 31886 1ogsA 497 9.55e+00 b.71.1.2,c.1.8.3 86997,86998 1xizA 159 9.95e+00 1ewqA 765 1.01e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1psuA 140 1.06e+01 d.38.1.5 88285 1vljA 407 1.07e+01 e.22.1.2 108832 1jdrA 294 1.07e+01 1ryc a.93.1.1 62908 1wvcA 259 1.11e+01 1e1oA 504 1.12e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1qx4A 274 1.15e+01 b.43.4.2,c.25.1.1 104624,104625 3proC 166 1.17e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1v4pA 157 1.18e+01 2aioA 269 1.19e+01 2aneA 125 1.24e+01 1g5cA 170 1.25e+01 1g5cA c.53.2.1 60264 1ejxC 567 1.26e+01 b.92.1.1,c.1.9.2 83184,83185 1yc9A 442 1.26e+01 1pfsA 78 1.29e+01 1pfsA b.40.4.7 25391 1o20A 427 1.29e+01 c.82.1.1 86556 1ixlA 131 1.31e+01 d.38.1.5 90717 1lylA 504 1.36e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1gv3A 248 1.48e+01 a.2.11.1,d.44.1.1 70585,70586 1vm7A 311 1.49e+01 c.72.1.1 108884 1a8rA 221 1.51e+01 1a8rA d.96.1.1 40587 1smlA 269 1.57e+01 1smlA d.157.1.1 42053 1xipA 388 1.60e+01 1wtaA 275 1.61e+01 1snzA 344 1.63e+01 b.30.5.4 98930 1i1nA 226 1.63e+01 c.66.1.7 71102 1iznB 277 1.64e+01 e.43.1.2 83848 1rsy 152 1.64e+01 1rsy b.7.1.2 23192 1rzuA 485 1.65e+01 c.87.1.8 105140 1izmA 184 1.72e+01 a.199.1.1 90725 1wudA 89 1.74e+01 1u3wA 374 1.78e+01 2f4nA 273 1.78e+01 1q15A 503 1.80e+01 c.26.2.1,d.153.1.1 95538,95539 2c4xA 260 1.83e+01 1rl0A 255 1.85e+01 1dazC 99 1.85e+01 1hvc b.50.1.1 26501 1kay 381 1.88e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2aliA 158 1.90e+01 1vl2A 421 1.90e+01 c.26.2.1,d.210.1.1 108708,108709 1y791 680 1.91e+01 1wekA 217 1.98e+01 2af4C 333 1.99e+01 1r5eA 115 2.06e+01 2a35A 215 2.09e+01 1nrjB 218 2.11e+01 c.37.1.8 86125 1wycA 392 2.13e+01 1zbyA 294 2.15e+01 1umkA 275 2.15e+01 1lj5A 379 2.19e+01 e.1.1.1 73928 1bupA 386 2.24e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ab8A 220 2.25e+01 1azsA d.58.29.1 39414 1on3A 523 2.30e+01 c.14.1.4,c.14.1.4 87107,87108 1h9sA 140 2.34e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2fkbA 180 2.36e+01 1jb7A 495 2.39e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1xjvA 294 2.45e+01 2fn0A 437 2.49e+01 1dykA 394 2.50e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1alu 186 2.51e+01 1alu a.26.1.1 16826 1jhjA 171 2.56e+01 b.18.1.9 66714 1fjgK 129 2.58e+01 1fjfK c.55.4.1 33733 1ogdA 131 2.58e+01 c.133.1.1 92893 2g1lA 104 2.59e+01 1lp8A 254 2.60e+01 d.165.1.1 91082 1z5hA 780 2.62e+01 1z53A 294 2.64e+01 1sltA 134 2.67e+01 1c1lA b.29.1.3 24186 2fefA 294 2.68e+01 1q87A 221 2.69e+01 e.47.1.1 96192 1o97D 320 2.78e+01 c.26.2.3,c.31.1.2 81233,81234 1vi6A 208 2.81e+01 c.23.15.1 100736 1w8oA 601 2.83e+01 1zhhB 242 2.84e+01 2cw8A 537 2.85e+01 1jf9A 408 2.87e+01 1c0nA c.67.1.3 62931 1otfA 62 2.92e+01 1otfA d.80.1.1 39820 1kpf 126 2.94e+01 1kpf d.13.1.1 37507 1xjcA 169 2.97e+01 1nbwA 607 2.97e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2eutA 294 3.03e+01 1wybA 392 3.06e+01 1t6cA 315 3.09e+01 c.55.1.8,c.55.1.8 106558,106559 1nnsA 326 3.11e+01 c.88.1.1 85910 1i7pA 274 3.12e+01 b.43.4.2,c.25.1.1 66048,66049 1e94F 449 3.22e+01 1do0A c.37.1.20 32443 1wab 232 3.24e+01 1wab c.23.10.3 31341 1qfhA 212 3.24e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1lox 662 3.25e+01 1lox a.119.1.2,b.12.1.1 19238,23638 2etvA 346 3.30e+01 2gjgA 248 3.38e+01 1bvqA 141 3.39e+01 1bvqA d.38.1.1 38542 2d4qA 257 3.41e+01 1wosA 364 3.42e+01 b.44.2.1,d.250.1.1 109468,109469 2bjbA 462 3.45e+01 1yuwA 554 3.46e+01 1wcqA 601 3.48e+01 1rcy 151 3.49e+01 1rcy b.6.1.1 23018 1f08A 148 3.53e+01 1f08A d.89.1.2 59564 2a8yA 270 3.55e+01 1mkiA 330 3.59e+01 e.3.1.2 84994 1o17A 345 3.60e+01 a.46.2.1,c.27.1.1 80765,80766 1s0uA 408 3.61e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1hf8A 289 3.63e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1a7cA 379 3.64e+01 1sek e.1.1.1 42660 1vjrA 271 3.65e+01 c.108.1.14 100832 2b61A 377 3.69e+01 1kpeA 126 3.74e+01 1kpf d.13.1.1 37508 2d0oA 610 3.78e+01 1uwkA 557 3.79e+01 e.51.1.1 108065 1vh5A 148 3.80e+01 d.38.1.5 100642 1i1iP 681 3.81e+01 1i1iP d.92.1.5 40297 1ecmA 109 3.87e+01 1ecmA a.130.1.1 19492 1e2wA 251 3.93e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 2f2hA 773 3.96e+01 1w30A 201 4.01e+01 1oj6A 151 4.02e+01 a.1.1.2 93088 2lhb 149 4.11e+01 2fal a.1.1.2 15597 1pzsA 208 4.12e+01 b.1.8.1 104397 1g5aA 628 4.12e+01 b.71.1.1,c.1.8.1 65152,65153 1kv7A 488 4.14e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1qi7A 253 4.17e+01 1qi7A d.165.1.1 42210 1kdgA 546 4.18e+01 c.3.1.2,d.16.1.1 77337,77338 2c26A 260 4.18e+01 1ztdA 133 4.21e+01 1q5dA 419 4.22e+01 a.104.1.1 95891 1ku0A 388 4.23e+01 c.69.1.18 72994 1gzwA 134 4.26e+01 b.29.1.3 90535 1wthD 391 4.28e+01 1q1rA 431 4.32e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1jniA 123 4.34e+01 a.138.1.3 71761 1y1nA 291 4.37e+01 1ukkA 142 4.38e+01 d.227.1.1 99491 1ygaA 342 4.40e+01 1pjxA 314 4.41e+01 b.68.6.1 104167 1e1aA 314 4.46e+01 1e1aA b.68.6.1 59155 1srqA 341 4.46e+01 e.55.1.1 105967 1lo7A 141 4.46e+01 d.38.1.1 74144 1fi8A 228 4.50e+01 5ptp b.47.1.2 26374 2fsrA 195 4.52e+01 1j3aA 142 4.56e+01 c.21.1.1 77070 1bebA 162 4.63e+01 1bebA b.60.1.1 27115 1awd 94 4.66e+01 1awd d.15.4.1 37673 1pyoA 167 4.66e+01 c.17.1.1 95370 1jcfA 344 4.67e+01 c.55.1.1,c.55.1.1 62878,62879 1e9lA 377 4.68e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1q2yA 140 4.70e+01 d.108.1.1 95655 1vf8A 377 4.74e+01 2yhx 457 4.77e+01 2yhx i.12.1.1 46024 1tkeA 224 4.79e+01 2calA 154 4.87e+01 1twuA 139 4.90e+01 d.32.1.8 107413 1x8vA 455 4.91e+01 1urvA 190 4.95e+01 1ut0A 190 4.95e+01 a.1.1.2 108012 1od3A 168 4.96e+01 b.18.1.10 86825 1avyA 74 4.99e+01 1avyB h.1.17.1 45656 2gfgA 193 5.06e+01 1xe1A 116 5.08e+01 b.43.3.1 109571 1azsB 212 5.11e+01 1azsA d.58.29.1 39423 1gr0A 367 5.12e+01 c.2.1.3,d.81.1.3 70379,70380 1q3iA 214 5.13e+01 d.220.1.1 104524 2bw8A 227 5.20e+01 1pj5A 830 5.20e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1ryiA 382 5.21e+01 1xsjA 778 5.25e+01 1f2rI 100 5.27e+01 1c9fA d.15.2.1 37641 1mbmA 198 5.29e+01 b.47.1.3 78916 1by2 119 5.32e+01 1by2 d.170.1.1 42452 1k8kE 178 5.34e+01 a.148.1.1 68311 1tt8A 164 5.43e+01 1dtoA 221 5.43e+01 1dtoA b.91.1.1 28405 1fw9A 164 5.45e+01 1fw9A d.190.1.1 60059 1e30A 155 5.48e+01 1rcy b.6.1.1 23016 1mkrA 294 5.52e+01 a.93.1.1 84997 1n13B 113 5.52e+01 1spf 35 5.53e+01 1spf j.35.1.1 46254 1uurA 473 5.58e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ym0A 238 5.66e+01 1ua4A 455 5.68e+01 c.72.1.3 99128 1c96A 753 5.68e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1x8hA 228 5.72e+01 1h2rL 534 5.75e+01 1h2rL e.18.1.1 43298 1p5zB 263 5.79e+01 c.37.1.1 87815 1k8tA 510 5.79e+01 e.41.1.1 68316 1xi3A 215 5.79e+01 c.1.3.1 109601 1k82A 268 5.84e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1es9A 232 5.85e+01 1wab c.23.10.3 31340 1qipA 183 5.86e+01 1qipA d.32.1.1 38470 1ykdA 398 5.86e+01 1ash 150 5.86e+01 1ash a.1.1.2 15622 1ftrA 296 5.87e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1fm4A 159 5.94e+01 1bv1 d.129.3.1 76186 1x8gA 227 5.95e+01 1wq3A 322 5.96e+01 1z94A 147 5.99e+01 1jogA 146 6.01e+01 a.24.16.2 77142 1c7qA 445 6.07e+01 2pgi c.80.1.2 35307 1wuiL 534 6.09e+01 8acn 754 6.11e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1lyqA 104 6.12e+01 b.1.18.17 78302 1gt1A 159 6.17e+01 b.60.1.1 90515 2bvyA 475 6.22e+01 1sk4A 163 6.22e+01 d.118.1.1 105664 1eexA 554 6.23e+01 1dioA c.1.19.3 29650 1kr7A 110 6.27e+01 a.1.1.4 72890 1txvA 452 6.28e+01 1dwkA 156 6.30e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 2blnA 305 6.35e+01 1wxxA 382 6.38e+01 1vllA 334 6.45e+01 c.2.1.13 108834 1fezA 256 6.46e+01 1fezA c.108.1.3 43343 1w6nA 134 6.63e+01 1bdo 80 6.68e+01 1bdo b.84.1.1 28214 1h0bA 256 6.72e+01 b.29.1.11 83422 2fymA 431 6.78e+01 1ubkL 534 6.82e+01 e.18.1.1 88422 1b8fA 509 6.84e+01 1b8fA a.127.1.2 19434 1difA 99 6.85e+01 1fmb b.50.1.1 26503 1n26A 325 6.86e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1fmtA 314 6.90e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1q1fA 151 6.95e+01 a.1.1.2 104476 2a5vA 213 6.95e+01 2bf6A 449 7.06e+01 1g7nA 131 7.11e+01 b.60.1.2 83274 1v1qA 134 7.13e+01 1iuhA 198 7.17e+01 d.61.1.2 83711 1k66A 149 7.20e+01 c.23.1.1 90941 1v10A 521 7.20e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2a74A 643 7.23e+01 1wocA 103 7.27e+01 1senA 164 7.33e+01 c.47.1.1 105465 1o0wA 252 7.43e+01 a.149.1.1,d.50.1.1 80751,80752 1p1lA 102 7.46e+01 d.58.5.2 87695 1yb3A 175 7.50e+01 1zvpA 133 7.50e+01 1ogpA 393 7.55e+01 b.1.18.6,d.176.1.1 92927,92928 1odfA 290 7.58e+01 c.37.1.6 92782 1uj6A 227 7.59e+01 c.124.1.4,d.58.40.1 107898,107899 1o6sB 105 7.61e+01 b.1.6.1 81096 1swvA 267 7.62e+01 1jovA 270 7.62e+01 b.30.5.7 84192 1gkmA 509 7.68e+01 a.127.1.2 70228 1ue1A 164 7.70e+01 b.40.4.3 99243 1b06A 210 7.74e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 2b30A 301 7.74e+01 2aifA 135 7.77e+01 1t9xA 1049 7.79e+01 1cl8A 276 7.79e+01 1ckqA c.52.1.1 33230 2aukA 190 7.81e+01 1p7tA 731 7.85e+01 c.1.13.1 94319 1nzaA 103 7.88e+01 d.58.5.2 86444 1z54A 132 7.88e+01 1s4bP 674 7.89e+01 d.92.1.5 105252 1vlyA 338 8.00e+01 b.44.2.1,d.250.1.1 108871,108872 1yphC 131 8.01e+01 1tdtA 259 8.02e+01 3tdt b.81.1.2 28055 1o8bA 219 8.03e+01 c.124.1.4,d.58.40.1 81180,81181 1fcyA 236 8.06e+01 2lbd a.123.1.1 19282 1ualA 274 8.06e+01 c.116.1.4 88383 2freA 200 8.15e+01 2go8A 122 8.15e+01 1f9zA 135 8.17e+01 1qipA d.32.1.1 38484 2sli 679 8.19e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1kgdA 180 8.20e+01 c.37.1.1 68582 2biqA 219 8.20e+01 2bvbA 137 8.20e+01 1hdmB 193 8.20e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 1oyeA 1049 8.22e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1ew2A 513 8.27e+01 1b8jA c.76.1.1 59525 1jp4A 308 8.34e+01 1jp4A e.7.1.1 63223 1hv9A 456 8.38e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1y07A 128 8.44e+01 1rq2A 382 8.52e+01 c.32.1.1,d.79.2.1 105048,105049 1m5yA 408 8.56e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1fa8A 135 8.57e+01 1qipA d.32.1.1 38486 1w96A 554 8.57e+01 1puzA 82 8.57e+01 a.218.1.1 104320 1kq3A 376 8.62e+01 e.22.1.2 68790 1ig8A 486 8.68e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1f1uA 323 8.69e+01 d.32.1.3,d.32.1.3 83200,83201 1ezwA 349 8.74e+01 1ezwA c.1.16.3 29558 1ylnA 252 8.76e+01 1ka2A 499 8.78e+01 d.92.1.5 77305 1oohA 126 8.78e+01 a.39.2.1 93383 2bgkA 278 8.79e+01 1sc3A 178 8.79e+01 c.17.1.1 105416 1vliA 385 8.80e+01 b.85.1.1,c.1.10.6 108830,108831 1txyA 104 8.83e+01 1p5dX 463 8.84e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1s72W 154 8.84e+01 d.59.1.1 105342 1atiA 505 8.84e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1zvnA 99 8.87e+01 1wc9A 169 8.92e+01 1jj2V 154 8.92e+01 1ffkT d.59.1.1 63107 1rreA 200 8.94e+01 d.14.1.10 97791 1sz7A 200 8.95e+01 1wqsA 173 8.96e+01