# List of top-scoring protein chains for t06-100-30-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 1xubA 298 3.87e-03 2gkeA 274 4.87e-02 1gqzA 274 6.26e-02 d.21.1.1,d.21.1.1 83311,83312 1p3dA 475 7.91e-02 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1dp4A 435 1.13e-01 1dp4A c.93.1.1 35710 1j5pA 253 2.67e-01 d.81.1.3,c.2.1.3 71577,83092 1rzhL 281 5.74e-01 f.26.1.1 98164 1nnxA 109 9.46e-01 b.40.10.1 92013 1vdkA 466 9.73e-01 a.127.1.1 100561 1t6aA 126 1.07e+00 d.129.8.1 106555 1sr8A 298 1.14e+00 e.54.1.1 105959 1gtzA 156 1.22e+00 c.23.13.1 70539 1qx4A 274 1.30e+00 b.43.4.2,c.25.1.1 104624,104625 1josA 128 1.52e+00 d.52.7.1 84191 1dkmA 410 1.53e+00 1dklA c.60.1.2 34000 1dkqA 410 1.57e+00 1dklA c.60.1.2 33998 1jc9A 269 1.70e+00 d.171.1.1 66490 1b56 135 2.37e+00 1hmt b.60.1.2 27183 1umkA 275 2.64e+00 1sziA 247 2.74e+00 a.24.23.1 106159 1kk1A 410 2.76e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1tafB 70 2.78e+00 1tafB a.22.1.3 16482 1mxmA 254 2.82e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1ecfA 504 3.03e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1oe4A 247 3.17e+00 c.18.1.3 86895 1hp1A 516 3.30e+00 d.114.1.1,d.159.1.2 70976,70977 1evhA 112 3.40e+00 1evhA b.55.1.4 26997 1g5cA 170 3.52e+00 1g5cA c.53.2.1 60264 1ixlA 131 3.84e+00 d.38.1.5 90717 1e1oA 504 4.12e+00 1lylA b.40.4.1,d.104.1.1 25258,40714 4uagA 437 4.28e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1xttA 216 4.64e+00 1f3uA 118 4.72e+00 1f3uA b.65.1.1 27521 3proC 166 5.33e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1pfsA 78 5.35e+00 1pfsA b.40.4.7 25391 1ogsA 497 5.55e+00 b.71.1.2,c.1.8.3 86997,86998 1o20A 427 5.73e+00 c.82.1.1 86556 1iznB 277 6.12e+00 e.43.1.2 83848 1izmA 184 6.14e+00 a.199.1.1 90725 1vljA 407 6.46e+00 e.22.1.2 108832 1snzA 344 6.53e+00 b.30.5.4 98930 1go4A 205 6.79e+00 d.135.1.1 70292 1jf9A 408 6.91e+00 1c0nA c.67.1.3 62931 1vl2A 421 7.18e+00 c.26.2.1,d.210.1.1 108708,108709 1jcfA 344 7.46e+00 c.55.1.1,c.55.1.1 62878,62879 1i1nA 226 7.52e+00 c.66.1.7 71102 1rsy 152 7.86e+00 1rsy b.7.1.2 23192 1ab8A 220 7.89e+00 1azsA d.58.29.1 39414 1yc9A 442 8.07e+00 1a8rA 221 8.23e+00 1a8rA d.96.1.1 40587 1ogdA 131 8.74e+00 c.133.1.1 92893 1rzuA 485 9.03e+00 c.87.1.8 105140 1jhjA 171 9.29e+00 b.18.1.9 66714 1r5eA 115 9.64e+00 1jb7A 495 9.77e+00 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1o17A 345 9.85e+00 a.46.2.1,c.27.1.1 80765,80766 1bupA 386 1.03e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1nnsA 326 1.06e+01 c.88.1.1 85910 1q15A 503 1.10e+01 c.26.2.1,d.153.1.1 95538,95539 1ejxC 567 1.11e+01 b.92.1.1,c.1.9.2 83184,83185 1q87A 221 1.12e+01 e.47.1.1 96192 1n13B 113 1.16e+01 1rl0A 255 1.17e+01 1alu 186 1.21e+01 1alu a.26.1.1 16826 1t6cA 315 1.21e+01 c.55.1.8,c.55.1.8 106558,106559 1qfhA 212 1.32e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1v4pA 157 1.33e+01 1xjvA 294 1.33e+01 1uwkA 557 1.34e+01 e.51.1.1 108065 1ash 150 1.41e+01 1ash a.1.1.2 15622 1kdgA 546 1.42e+01 c.3.1.2,d.16.1.1 77337,77338 1sk4A 163 1.48e+01 d.118.1.1 105664 1o97D 320 1.50e+01 c.26.2.3,c.31.1.2 81233,81234 1lj5A 379 1.53e+01 e.1.1.1 73928 1fjgK 129 1.54e+01 1fjfK c.55.4.1 33733 1ecmA 109 1.55e+01 1ecmA a.130.1.1 19492 1fm4A 159 1.65e+01 1bv1 d.129.3.1 76186 1ubkL 534 1.70e+01 e.18.1.1 88422 1nbwA 607 1.73e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1pyoA 167 1.73e+01 c.17.1.1 95370 1gt1A 159 1.75e+01 b.60.1.1 90515 1qipA 183 1.78e+01 1qipA d.32.1.1 38470 1pzsA 208 1.81e+01 b.1.8.1 104397 1ig8A 486 1.90e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1f08A 148 1.92e+01 1f08A d.89.1.2 59564 1v8yA 170 1.94e+01 1kpf 126 1.95e+01 1kpf d.13.1.1 37507 1on3A 523 1.95e+01 c.14.1.4,c.14.1.4 87107,87108 1pjxA 314 1.99e+01 b.68.6.1 104167 1avyA 74 2.01e+01 1avyB h.1.17.1 45656 1kv7A 488 2.01e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1hf8A 289 2.04e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1g7nA 131 2.08e+01 b.60.1.2 83274 1rybA 212 2.09e+01 c.56.3.1 98098 1g5aA 628 2.10e+01 b.71.1.1,c.1.8.1 65152,65153 1tkeA 224 2.14e+01 1vh5A 148 2.18e+01 d.38.1.5 100642 1j3aA 142 2.19e+01 c.21.1.1 77070 1mkiA 330 2.22e+01 e.3.1.2 84994 1dykA 394 2.22e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1dwkA 156 2.33e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1bdo 80 2.35e+01 1bdo b.84.1.1 28214 1otfA 62 2.36e+01 1otfA d.80.1.1 39820 1ku0A 388 2.41e+01 c.69.1.18 72994 1awd 94 2.43e+01 1awd d.15.4.1 37673 1rreA 200 2.47e+01 d.14.1.10 97791 1e30A 155 2.48e+01 1rcy b.6.1.1 23016 1q1rA 431 2.51e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1srqA 341 2.54e+01 e.55.1.1 105967 1tt8A 164 2.56e+01 1ftrA 296 2.61e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1k8kE 178 2.66e+01 a.148.1.1 68311 1rypD 241 2.69e+01 1rypD d.153.1.4 41935 1f1uA 323 2.70e+01 d.32.1.3,d.32.1.3 83200,83201 1q1fA 151 2.70e+01 a.1.1.2 104476 1e2wA 251 2.75e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1eexA 554 2.91e+01 1dioA c.1.19.3 29650 1lyqA 104 2.94e+01 b.1.18.17 78302 1bebA 162 2.94e+01 1bebA b.60.1.1 27115 2gfgA 193 2.95e+01 1x8vA 455 2.98e+01 1pj5A 830 3.00e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1gr0A 367 3.01e+01 c.2.1.3,d.81.1.3 70379,70380 1p5zB 263 3.03e+01 c.37.1.1 87815 1c96A 753 3.04e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1k82A 268 3.05e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1spf 35 3.05e+01 1spf j.35.1.1 46254 1p7tA 731 3.14e+01 c.1.13.1 94319 2sli 679 3.15e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1ryiA 382 3.18e+01 1j1iA 296 3.19e+01 c.69.1.10 83977 1q2yA 140 3.20e+01 d.108.1.1 95655 1jniA 123 3.26e+01 a.138.1.3 71761 1kr7A 110 3.29e+01 a.1.1.4 72890 1x8gA 227 3.36e+01 1od3A 168 3.40e+01 b.18.1.10 86825 1kgdA 180 3.48e+01 c.37.1.1 68582 1mvfD 82 3.48e+01 b.129.1.1 85143 1lo7A 141 3.53e+01 d.38.1.1 74144 1kq3A 376 3.56e+01 e.22.1.2 68790 1q3iA 214 3.57e+01 d.220.1.1 104524 1ezwA 349 3.58e+01 1ezwA c.1.16.3 29558 1fcyA 236 3.59e+01 2lbd a.123.1.1 19282 1f9zA 135 3.61e+01 1qipA d.32.1.1 38484 1tueB 218 3.67e+01 b.91.1.1 107324 1q5dA 419 3.69e+01 a.104.1.1 95891 1ukkA 142 3.82e+01 d.227.1.1 99491 1ghpA 258 3.82e+01 1btl e.3.1.1 60520 1gycA 499 3.89e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1iicA 422 3.89e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1swvA 267 3.90e+01 1ebfA 358 3.99e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1c7qA 445 4.01e+01 2pgi c.80.1.2 35307 1jl0A 334 4.01e+01 1jenA d.156.1.1 63155 1sc3A 178 4.04e+01 c.17.1.1 105416 1rm6A 769 4.05e+01 1oohA 126 4.08e+01 a.39.2.1 93383 1mqvA 125 4.08e+01 a.24.3.2 79415 2blnA 305 4.09e+01 1o75A 415 4.10e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1by2 119 4.12e+01 1by2 d.170.1.1 42452 1o5zA 442 4.19e+01 c.59.1.2,c.72.2.2 92530,92531 1et9A 204 4.19e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1cl8A 276 4.27e+01 1ckqA c.52.1.1 33230 1k66A 149 4.28e+01 c.23.1.1 90941 1yb3A 175 4.28e+01 1es9A 232 4.33e+01 1wab c.23.10.3 31340 1b06A 210 4.35e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1jogA 146 4.37e+01 a.24.16.2 77142 1rjoA 646 4.40e+01 1nscA 390 4.42e+01 2qwc b.68.1.1 27591 1s4bP 674 4.47e+01 d.92.1.5 105252 1prxA 224 4.51e+01 1prxA c.47.1.10 33076 1ka2A 499 4.53e+01 d.92.1.5 77305 1o6sB 105 4.56e+01 b.1.6.1 81096 1sz7A 200 4.66e+01 1fmtA 314 4.67e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1o8bA 219 4.72e+01 c.124.1.4,d.58.40.1 81180,81181 1yg9A 330 4.79e+01 1gkmA 509 4.80e+01 a.127.1.2 70228 1flmA 122 4.80e+01 1axj b.45.1.1 25747 1w9aA 147 5.03e+01 2gqrA 237 5.06e+01 1q5zA 177 5.07e+01 a.196.1.1 95954 1xrkA 124 5.14e+01 1nrjB 218 5.17e+01 c.37.1.8 86125 1seiA 130 5.21e+01 1seiA d.140.1.1 41463 1n26A 325 5.31e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1mzyA 333 5.35e+01 b.6.1.3,b.6.1.3 103848,103849 1ri6A 343 5.38e+01 b.69.11.1 97503 1bu6O 501 5.39e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1g8pA 350 5.40e+01 1g8pA c.37.1.20 60376 1jp4A 308 5.41e+01 1jp4A e.7.1.1 63223 1nnhA 294 5.46e+01 d.104.1.1 92005 1h4xA 117 5.51e+01 1auz c.13.2.1 60626 1hbnC 248 5.56e+01 1mroC d.58.31.1 60902 1m0uA 249 5.62e+01 a.45.1.1,c.47.1.5 78359,78360 1w96A 554 5.67e+01 1rq2A 382 5.71e+01 c.32.1.1,d.79.2.1 105048,105049 1snrA 341 5.75e+01 b.6.1.3,b.6.1.3 105823,105824 1ckmA 330 5.76e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1r59O 505 5.76e+01 1r69 69 5.78e+01 1r69 a.35.1.2 17028 1cd3B 120 5.81e+01 1cd3B 1ydyA 356 5.85e+01 1q4gA 553 5.90e+01 a.93.1.2,g.3.11.1 95789,95790 1vhqA 232 5.91e+01 c.23.16.2 100696 1su0B 159 5.93e+01 d.224.1.2 106015 1oxdA 227 5.93e+01 d.22.1.1 93687 1odfA 290 5.96e+01 c.37.1.6 92782 1jovA 270 5.97e+01 b.30.5.7 84192 1q2zA 120 5.99e+01 a.118.19.1 95656 1lshA 1056 6.02e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1m2oA 768 6.02e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1vlyA 338 6.05e+01 b.44.2.1,d.250.1.1 108871,108872 2cfuA 658 6.06e+01 1p5dX 463 6.06e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2ga9D 469 6.09e+01 1gyoA 109 6.12e+01 a.138.1.1 70763 1avbA 226 6.14e+01 1led b.29.1.1 24158 1o5xA 248 6.15e+01 c.1.1.1 92528 1gskA 513 6.20e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1t0qC 86 6.22e+01 d.15.12.1 106222 2biqA 219 6.34e+01 1a91 79 6.34e+01 1a91 f.17.1.1 43635 1fcdA 401 6.42e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1s12A 94 6.50e+01 1senA 164 6.60e+01 c.47.1.1 105465 1npyA 271 6.63e+01 c.2.1.7,c.58.1.5 85995,85996 1sknP 92 6.65e+01 1sknP a.37.1.1 17127 1rmg 422 6.65e+01 1rmg b.80.1.3 28029 1moq 368 6.74e+01 1moq c.80.1.1 35302 1i2aA 219 6.74e+01 e.24.1.1 90660 1at3A 247 6.77e+01 1at3A b.57.1.1 27021 1tfe 145 6.87e+01 1tfe d.43.1.1 38680 1v9yA 167 6.91e+01 d.110.3.2 108454 1t0bA 252 6.98e+01 c.23.16.6 106199 1xe7A 203 7.04e+01 1bec 238 7.06e+01 1bec b.1.1.1,b.1.1.2 20627,21561 1c4rA 182 7.11e+01 1c4rA b.29.1.4 24229 1mngA 203 7.15e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1ogoX 574 7.21e+01 b.133.1.1,b.80.1.10 92925,92926 1fuxA 166 7.25e+01 1fjjA b.17.1.2 60034 1rt8A 513 7.28e+01 a.40.1.1 105095 1r2zA 274 7.35e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1ehiA 377 7.40e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1mi3A 322 7.45e+01 c.1.7.1 91274 1f2tA 149 7.50e+01 1f2tA c.37.1.12 32373 1a8q 274 7.50e+01 1brt c.69.1.12 34702 1jae 471 7.57e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1tuhA 156 7.57e+01 d.17.4.11 107345 1hg8A 349 7.58e+01 b.80.1.3 65830 1ru3A 732 7.61e+01 e.26.1.3 97835 1jbiA 100 7.61e+01 d.209.1.1 66481 1v8hA 107 7.63e+01 1nzaA 103 7.63e+01 d.58.5.2 86444 1h3fA 432 7.64e+01 c.26.1.1,d.66.1.4 76631,76632 1xkpB 124 7.68e+01 1c0pA 363 7.71e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1i4uA 181 7.77e+01 b.60.1.1 61732 1mbmA 198 7.84e+01 b.47.1.3 78916 1r5mA 425 7.86e+01 1eueA 86 7.87e+01 1cyo d.120.1.1 59504 1esxA 96 7.89e+01 1esxA j.11.1.1 59501 1qe5A 266 7.93e+01 1b8oA c.56.2.1 33784 1nn5A 215 8.08e+01 c.37.1.1 85892 1oo0A 147 8.15e+01 d.232.1.1 87182 1p1lA 102 8.17e+01 d.58.5.2 87695 1lwdA 413 8.25e+01 c.77.1.1 78265 1szoA 257 8.31e+01 c.14.1.3 106164 1gk9B 557 8.31e+01 1wvgA 359 8.35e+01 1u7iA 136 8.36e+01 d.32.1.7 107724 1iwmA 186 8.37e+01 b.125.1.2 83758 1uxzA 131 8.43e+01 b.18.1.10 100170 1f3uB 171 8.50e+01 1f3uB b.65.1.1 27525 1je5A 206 8.51e+01 1je5A b.40.4.7 62909 1qb5D 99 8.52e+01 b.40.2.1 88357 1gtmA 419 8.53e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1nkiA 135 8.57e+01 d.32.1.2 91941 1jhdA 396 8.58e+01 b.122.1.3,c.26.1.5 66712,66713 1khtA 192 8.65e+01 c.37.1.1 84401 1omoA 322 8.67e+01 c.2.1.13 104017 1mkyA 439 8.70e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1oe1A 336 8.73e+01 b.6.1.3,b.6.1.3 86891,86892 1ivnA 190 8.75e+01 c.23.10.5 83719 1s2oA 244 8.76e+01 1v2bA 177 8.78e+01 d.107.1.2 108279 1h99A 224 8.93e+01 a.142.1.1,a.142.1.1 60814,60815 1x9dA 538 9.00e+01