# 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 1gqzA 274 4.22e-06 d.21.1.1,d.21.1.1 83311,83312 2gkeA 274 5.14e-06 1w61A 414 4.36e-05 1bwzA 274 4.77e-05 1bwzA d.21.1.1,d.21.1.1 38337,38338 1u1wA 298 4.34e-03 1tm0A 350 4.91e-03 d.21.1.3 107147 1t6kA 278 1.09e-02 1xubA 298 1.54e-02 1qyaA 307 4.39e-02 d.21.1.2,d.21.1.2 104653,104654 1sdjA 310 6.06e-02 d.21.1.2,d.21.1.2 98807,98808 1o0pA 104 1.17e-01 d.58.7.1 86535 1z94A 147 1.48e-01 1dp4A 435 2.96e-01 1dp4A c.93.1.1 35710 1sr8A 298 4.94e-01 e.54.1.1 105959 1xttA 216 5.34e-01 1pj5A 830 6.08e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2bw0A 329 8.29e-01 1nscA 390 8.68e-01 2qwc b.68.1.1 27591 2sli 679 8.90e-01 2sli b.29.1.9,b.68.1.1 24274,27611 1wekA 217 1.06e+00 1o17A 345 1.11e+00 a.46.2.1,c.27.1.1 80765,80766 2calA 154 1.51e+00 1v58A 241 1.67e+00 c.47.1.9,d.17.3.1 108371,108372 2g6yA 217 1.76e+00 1h0bA 256 2.06e+00 b.29.1.11 83422 1a8rA 221 2.20e+00 1a8rA d.96.1.1 40587 1p3dA 475 2.32e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1vhzA 198 2.35e+00 d.113.1.1 100718 1oe4A 247 2.53e+00 c.18.1.3 86895 1mkeA 152 2.63e+00 b.55.1.4 79231 1vrmA 325 2.66e+00 1ogsA 497 2.66e+00 b.71.1.2,c.1.8.3 86997,86998 1k3bB 164 2.71e+00 d.3.1.1 72015 1josA 128 2.71e+00 d.52.7.1 84191 2fclA 169 2.92e+00 1ym5A 300 3.16e+00 2bw8A 227 3.19e+00 1rec 201 3.43e+00 1rec a.39.1.5 17326 1omrA 201 3.47e+00 a.39.1.5 93349 1d0iA 156 3.52e+00 2dhqA c.23.13.1 31383 2gjgA 248 3.66e+00 1f2rI 100 3.70e+00 1c9fA d.15.2.1 37641 1e30A 155 3.74e+00 1rcy b.6.1.1 23016 2f6uA 234 3.75e+00 1lj5A 379 3.86e+00 e.1.1.1 73928 1wznA 252 4.33e+00 1qwnA 1045 4.39e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1zwxA 301 4.40e+00 1ycoA 279 4.43e+00 2ewrA 170 4.67e+00 1cwvA 492 4.87e+00 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1bupA 386 5.03e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1gtzA 156 5.32e+00 c.23.13.1 70539 1rcy 151 5.40e+00 1rcy b.6.1.1 23018 1ci3M 249 5.55e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1kay 381 5.55e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1ihp 438 5.70e+00 1ihp c.60.1.2 33993 1vdkA 466 6.21e+00 a.127.1.1 100561 1xo1A 291 6.86e+00 1exnA a.60.7.1,c.120.1.2 18086,33356 1j5pA 253 6.98e+00 d.81.1.3,c.2.1.3 71577,83092 1o8bA 219 7.49e+00 c.124.1.4,d.58.40.1 81180,81181 1mkiA 330 7.83e+00 e.3.1.2 84994 1oc2A 348 8.74e+00 c.2.1.2 92765 2b3nA 159 8.75e+00 1oa4A 222 8.77e+00 b.29.1.11 86731 1vljA 407 8.85e+00 e.22.1.2 108832 7fd1A 106 8.99e+00 1a6l d.58.1.2 38953 1q15A 503 9.09e+00 c.26.2.1,d.153.1.1 95538,95539 2cw8A 537 9.30e+00 1kepA 348 9.45e+00 c.2.1.2 68536 1y0gA 191 9.47e+00 1ut9A 609 9.56e+00 a.102.1.2,b.1.18.2 99912,99913 1s1qA 145 9.69e+00 d.20.1.2 98351 1htyA 1015 9.76e+00 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1m3yA 413 9.94e+00 b.121.2.3,b.121.2.3 78579,78580 2fr2A 172 1.06e+01 1orrA 347 1.09e+01 c.2.1.2 93460 1bqsA 209 1.11e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1ux8A 132 1.25e+01 1dmhA 311 1.27e+01 1dmhA b.3.6.1 22633 1dlwA 116 1.28e+01 1dlyA a.1.1.1 14982 1nnxA 109 1.29e+01 b.40.10.1 92013 1lm6A 215 1.29e+01 d.167.1.1 84628 1tafB 70 1.32e+01 1tafB a.22.1.3 16482 2aliA 158 1.33e+01 1r44A 202 1.36e+01 d.65.1.4 104787 1r7lA 110 1.37e+01 d.277.1.1 104837 1lt3A 240 1.39e+01 1lt3A d.166.1.1 42230 1ufbA 127 1.41e+01 a.24.16.3 99331 2azpA 318 1.42e+01 1ut8A 291 1.43e+01 a.60.7.1,c.120.1.2 99908,99909 1vl2A 421 1.47e+01 c.26.2.1,d.210.1.1 108708,108709 1zo2A 129 1.53e+01 1kkcA 221 1.54e+01 a.2.11.1,d.44.1.1 68660,68661 2aioA 269 1.55e+01 1f3uA 118 1.59e+01 1f3uA b.65.1.1 27521 1xtqA 177 1.63e+01 1br9 194 1.65e+01 1br9 b.40.3.1 25235 2aneA 125 1.71e+01 1avyA 74 1.74e+01 1avyB h.1.17.1 45656 2f15A 96 1.76e+01 1p1mA 406 1.78e+01 b.92.1.4,c.1.9.9 87696,87697 1i1iP 681 1.79e+01 1i1iP d.92.1.5 40297 1mngA 203 1.80e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1uctA 218 1.80e+01 b.1.1.4,b.1.1.4 88467,88468 2cr4A 126 1.80e+01 1sv6A 269 1.82e+01 d.177.1.1 106043 1ynfA 458 1.85e+01 1qhkA 47 1.87e+01 1qhkA d.100.1.2 40694 1gmiA 136 1.90e+01 b.7.1.1 65309 2g6tA 306 1.90e+01 2b59B 172 1.93e+01 1mpp 361 1.97e+01 2rmpA b.50.1.2 26856 1jjiA 311 2.00e+01 c.69.1.2 66766 1u84A 90 2.02e+01 1mo9A 523 2.03e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2ckiA 262 2.03e+01 1uisA 231 2.04e+01 d.22.1.1 99431 2a8yA 270 2.04e+01 2dcyA 185 2.05e+01 1prxA 224 2.10e+01 1prxA c.47.1.10 33076 1ygs 234 2.16e+01 1ygs b.26.1.1 23907 2f4nA 273 2.17e+01 1w34A 304 2.19e+01 2bsaA 303 2.20e+01 1m0dA 138 2.21e+01 c.52.1.17 74354 1tdtA 259 2.21e+01 3tdt b.81.1.2 28055 2bvbA 137 2.22e+01 1otgA 125 2.23e+01 1otgA d.80.1.2 39831 1j6pA 418 2.23e+01 b.92.1.4,c.1.9.9 77089,77090 1wosA 364 2.23e+01 b.44.2.1,d.250.1.1 109468,109469 1gv3A 248 2.32e+01 a.2.11.1,d.44.1.1 70585,70586 1a7cA 379 2.33e+01 1sek e.1.1.1 42660 1dqqB 210 2.34e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 1x99A 145 2.40e+01 1ogiA 303 2.44e+01 b.43.4.2,c.25.1.1 92914,92915 1rzhL 281 2.47e+01 f.26.1.1 98164 1sziA 247 2.50e+01 a.24.23.1 106159 1hekA 131 2.53e+01 a.61.1.5 65818 2pil 159 2.56e+01 2pil d.24.1.1 38376 1x6zA 123 2.57e+01 1y7wA 291 2.63e+01 2gdzA 267 2.65e+01 1twuA 139 2.65e+01 d.32.1.8 107413 1mqoA 227 2.73e+01 d.157.1.1 103846 1js8A 394 2.74e+01 a.86.1.1,b.112.1.1 67219,67220 1oo0A 147 2.76e+01 d.232.1.1 87182 1smlA 269 2.84e+01 1smlA d.157.1.1 42053 1i2aA 219 2.84e+01 e.24.1.1 90660 1qipA 183 2.86e+01 1qipA d.32.1.1 38470 1yqfA 203 2.90e+01 2bh9A 489 2.91e+01 1t6cA 315 2.96e+01 c.55.1.8,c.55.1.8 106558,106559 1ltsA 185 2.97e+01 1lt3A d.166.1.1 42229 1szwA 379 2.99e+01 d.265.1.4 99047 1xnb 185 3.03e+01 1axkA b.29.1.11 24308 1cex 214 3.06e+01 1cex c.69.1.30 31285 1t6aA 126 3.06e+01 d.129.8.1 106555 2fz4A 237 3.08e+01 1mxmA 254 3.09e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1ffa 214 3.11e+01 1cex c.69.1.30 31289 1y791 680 3.15e+01 1z0nA 96 3.16e+01 1wudA 89 3.17e+01 1que 303 3.18e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1e1oA 504 3.18e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2nlrA 234 3.19e+01 2nlrA b.29.1.11 24344 1zm0A 114 3.19e+01 1alu 186 3.20e+01 1alu a.26.1.1 16826 1rzhM 307 3.24e+01 f.26.1.1 98165 1go2A 304 3.25e+01 b.43.4.2,c.25.1.1 76243,76244 1oq1A 223 3.28e+01 b.29.1.17 93408 1u2hA 99 3.28e+01 1byrA 155 3.29e+01 1byrA d.136.1.1 41450 1ooyA 481 3.31e+01 c.124.1.3,c.124.1.2 93388,93389 1j75A 67 3.34e+01 a.4.5.19 62673 3tdt 274 3.34e+01 3tdt b.81.1.2 28053 1mr7A 209 3.35e+01 b.81.1.3 91430 1wtaA 275 3.35e+01 1z54A 132 3.44e+01 1z53A 294 3.49e+01 1ru0A 105 3.51e+01 1yuwA 554 3.53e+01 1czfA 362 3.56e+01 1czfA b.80.1.3 28031 1m5yA 408 3.61e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1hf2A 210 3.66e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1a8i 842 3.67e+01 1a8i c.87.1.4 35490 1w6sA 599 3.68e+01 1f00I 282 3.69e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1pylA 97 3.70e+01 d.1.1.2 104391 1kxgA 152 3.73e+01 b.22.1.1 73145 1k66A 149 3.75e+01 c.23.1.1 90941 1qwdA 177 3.78e+01 b.60.1.1 96471 2gsq 202 3.84e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1h9dB 134 3.85e+01 2jhbA b.54.1.1 60822 1r5eA 115 3.90e+01 1p7tA 731 3.94e+01 c.1.13.1 94319 1xxnA 185 3.96e+01 2aieP 203 4.01e+01 1jdrA 294 4.03e+01 1ryc a.93.1.1 62908 1hyoA 421 4.05e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1q87A 221 4.06e+01 e.47.1.1 96192 2bx2L 517 4.08e+01 1y1nA 291 4.08e+01 2eutA 294 4.10e+01 1nksA 194 4.12e+01 1nksA c.37.1.1 31886 2beiA 170 4.13e+01 1ygaA 342 4.16e+01 1zn6A 227 4.19e+01 2cxcA 144 4.19e+01 1npyA 271 4.21e+01 c.2.1.7,c.58.1.5 85995,85996 2d4qA 257 4.25e+01 1vh5A 148 4.27e+01 d.38.1.5 100642 1jhjA 171 4.28e+01 b.18.1.9 66714 1ema 236 4.28e+01 1ema d.22.1.1 38339 1y43A 39 4.28e+01 1sr4C 166 4.34e+01 b.42.2.1 105950 1lylA 504 4.34e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1sotA 320 4.35e+01 b.36.1.4,b.47.1.1 105852,105853 1zz1A 369 4.38e+01 1zynA 202 4.41e+01 1nzaA 103 4.42e+01 d.58.5.2 86444 1awd 94 4.43e+01 1awd d.15.4.1 37673 1wkvA 389 4.45e+01 1pg4A 652 4.45e+01 e.23.1.1 88067 2madH 373 4.46e+01 2bbkH b.69.2.1 27639 1qi9A 556 4.51e+01 1qhbA a.111.1.2 19053 2phlA 397 4.66e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 2a6tA 271 4.67e+01 1wvqA 167 4.72e+01 1qfgA 725 4.74e+01 1by5A f.4.3.3 43803 1jihA 531 4.78e+01 d.240.1.1,e.8.1.7 90374,90375 1gci 269 4.80e+01 1gci c.41.1.1 32503 1dzoA 123 4.83e+01 1dzoA d.24.1.1 38378 2hrvA 142 4.86e+01 2hrvA b.47.1.4 26429 1gpiA 431 4.87e+01 b.29.1.10 65450 1yc9A 442 4.97e+01 1hf8A 289 4.97e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2gc9A 179 5.14e+01 1zbyA 294 5.15e+01 1dkzA 219 5.15e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2ai4A 119 5.19e+01 1nnsA 326 5.24e+01 c.88.1.1 85910 1dazC 99 5.39e+01 1hvc b.50.1.1 26501 1go4A 205 5.42e+01 d.135.1.1 70292 1odkA 235 5.51e+01 c.56.2.1 86863 1cqqA 180 5.54e+01 1cqqA b.47.1.4 26422 2erbA 125 5.54e+01 1e6yB 433 5.63e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1u3eM 174 5.66e+01 d.4.1.3,d.285.1.1 107640,107641 1b8fA 509 5.70e+01 1b8fA a.127.1.2 19434 1xe7A 203 5.81e+01 1iz6A 138 5.87e+01 b.34.5.2,b.40.4.5 76976,76977 1g8iA 190 5.87e+01 1rec a.39.1.5 60363 1yfqA 342 5.88e+01 1q06A 135 5.89e+01 a.6.1.3 95493 1z0mA 96 5.89e+01 1qjtA 99 5.91e+01 1eh2 a.39.1.6 17335 2et1A 201 5.94e+01 1fe0A 68 5.97e+01 1cc8A d.58.17.1 39345 1h09A 338 5.98e+01 b.109.1.1,c.1.8.8 83420,83421 2g1uA 155 6.00e+01 1sc6A 404 6.01e+01 1gkmA 509 6.09e+01 a.127.1.2 70228 1fzrA 138 6.10e+01 1fzrA c.52.1.17 33336 1dszB 85 6.11e+01 2nllB g.39.1.2 45108 1f08A 148 6.14e+01 1f08A d.89.1.2 59564 1kbvA 327 6.15e+01 b.6.1.3,b.6.1.3 68395,68396 1tmxA 293 6.16e+01 2eifA 136 6.21e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1jc9A 269 6.39e+01 d.171.1.1 66490 1umkA 275 6.42e+01 1fi2A 201 6.43e+01 1fi2A b.82.1.2 59845 1euhA 475 6.46e+01 1euhA c.82.1.1 35369 2a35A 215 6.48e+01 1lk5A 229 6.49e+01 c.124.1.4,d.58.40.1 73960,73961 1wbpA 397 6.62e+01 1q1rA 431 6.67e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1qx4A 274 6.70e+01 b.43.4.2,c.25.1.1 104624,104625 1wcqA 601 6.71e+01 1mkrA 294 6.72e+01 a.93.1.1 84997 1ftrA 296 6.73e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1kpf 126 6.76e+01 1kpf d.13.1.1 37507 1y3nA 490 6.78e+01 1ogoX 574 6.84e+01 b.133.1.1,b.80.1.10 92925,92926 1eueA 86 6.87e+01 1cyo d.120.1.1 59504 1l5jA 865 6.90e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 2gaeA 346 6.94e+01 1hyuA 521 6.95e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1pzsA 208 6.97e+01 b.1.8.1 104397 1rb9 53 7.01e+01 1rb9 g.41.5.1 45214 1u9tA 354 7.07e+01 1rsy 152 7.20e+01 1rsy b.7.1.2 23192 1urvA 190 7.25e+01 1ut0A 190 7.25e+01 a.1.1.2 108012 2fo3A 125 7.31e+01 1os8A 223 7.37e+01 b.47.1.1 93481 1uwkA 557 7.41e+01 e.51.1.1 108065 1zhhB 242 7.42e+01 1j1nA 492 7.45e+01 c.94.1.1 83978 1a91 79 7.48e+01 1a91 f.17.1.1 43635 2cpgA 45 7.51e+01 2cpgA a.43.1.3 17455 1n0wA 243 7.51e+01 c.37.1.11 79772 1budA 197 7.52e+01 1atlA d.92.1.9 40328 1ko3A 230 7.60e+01 d.157.1.1 90974 1k2eA 156 7.60e+01 d.113.1.1 72010 1rzuA 485 7.66e+01 c.87.1.8 105140 1ciy 590 7.68e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1eo9A 209 7.69e+01 3pchA b.3.6.1 22731 1xewX 182 7.69e+01 1aun 208 7.70e+01 1thv b.25.1.1 23900 1dl5A 317 7.80e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1qwkA 317 7.80e+01 c.1.7.1 96482 2f6eA 127 7.89e+01 1ejxC 567 7.96e+01 b.92.1.1,c.1.9.2 83184,83185 1tueB 218 7.98e+01 b.91.1.1 107324 2fn0A 437 8.01e+01 1xtzA 264 8.02e+01 1vf8A 377 8.03e+01 1ouoA 210 8.03e+01 d.4.1.6 93554 1w8oA 601 8.09e+01 1eexA 554 8.15e+01 1dioA c.1.19.3 29650 2awkA 228 8.17e+01 1jtdB 273 8.19e+01 b.69.5.2 67265 1voqa 90 8.30e+01 1h8gA 95 8.33e+01 b.109.1.1 65735 1umzA 278 8.33e+01 b.29.1.2 99639 1c7qA 445 8.35e+01 2pgi c.80.1.2 35307 1bhdA 118 8.39e+01 1bkrA a.40.1.1 17398 1h5uA 842 8.40e+01 1a8i c.87.1.4 60655 1q5zA 177 8.42e+01 a.196.1.1 95954 2b0aA 186 8.47e+01 1dseA 292 8.49e+01 1ryc a.93.1.1 59130 1midA 91 8.51e+01 a.52.1.1 91280 1lox 662 8.54e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1nbwA 607 8.56e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1rzl 91 8.61e+01 1rzl a.52.1.1 17817 3proC 166 8.65e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1o5zA 442 8.68e+01 c.59.1.2,c.72.2.2 92530,92531 1zoyC 140 8.71e+01 1dtoA 221 8.77e+01 1dtoA b.91.1.1 28405 4uagA 437 8.78e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1zkiA 133 8.80e+01 2d0oA 610 8.85e+01 1bdo 80 8.85e+01 1bdo b.84.1.1 28214 1wraA 308 8.88e+01 1u3wA 374 8.89e+01 1ijyA 130 8.99e+01 1ijxA a.141.1.1 62517 1iqaA 160 9.00e+01 b.22.1.1 71274