# List of top-scoring protein chains for t06-100-30-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 2gkeA 274 4.84e-06 1gqzA 274 5.21e-06 d.21.1.1,d.21.1.1 83311,83312 1xubA 298 1.73e-02 1sdjA 310 6.99e-02 d.21.1.2,d.21.1.2 98807,98808 1qyaA 307 8.21e-02 d.21.1.2,d.21.1.2 104653,104654 1nscA 390 2.26e-01 2qwc b.68.1.1 27591 2sli 679 3.81e-01 2sli b.29.1.9,b.68.1.1 24274,27611 1sr8A 298 4.41e-01 e.54.1.1 105959 1dp4A 435 6.46e-01 1dp4A c.93.1.1 35710 1o17A 345 6.83e-01 a.46.2.1,c.27.1.1 80765,80766 1lj5A 379 1.03e+00 e.1.1.1 73928 1xttA 216 1.19e+00 1pj5A 830 1.38e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1dmhA 311 1.59e+00 1dmhA b.3.6.1 22633 1josA 128 1.62e+00 d.52.7.1 84191 1e30A 155 1.81e+00 1rcy b.6.1.1 23016 1vdkA 466 1.99e+00 a.127.1.1 100561 1bupA 386 2.17e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1v58A 241 2.37e+00 c.47.1.9,d.17.3.1 108371,108372 1omrA 201 2.39e+00 a.39.1.5 93349 1orrA 347 2.69e+00 c.2.1.2 93460 1p3dA 475 2.74e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1k3bB 164 2.88e+00 d.3.1.1 72015 1nnsA 326 2.90e+00 c.88.1.1 85910 1a8rA 221 2.93e+00 1a8rA d.96.1.1 40587 1r7lA 110 3.05e+00 d.277.1.1 104837 1ogsA 497 4.22e+00 b.71.1.2,c.1.8.3 86997,86998 1byrA 155 4.40e+00 1byrA d.136.1.1 41450 1mkiA 330 4.43e+00 e.3.1.2 84994 1qwnA 1045 4.48e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1qx4A 274 4.65e+00 b.43.4.2,c.25.1.1 104624,104625 1gtzA 156 4.82e+00 c.23.13.1 70539 1oa4A 222 4.91e+00 b.29.1.11 86731 1sc6A 404 5.05e+00 1gmiA 136 5.07e+00 b.7.1.1 65309 1rzhL 281 5.10e+00 f.26.1.1 98164 1oc2A 348 6.39e+00 c.2.1.2 92765 1vrmA 325 6.53e+00 1szwA 379 6.53e+00 d.265.1.4 99047 1oe4A 247 6.64e+00 c.18.1.3 86895 1dlwA 116 6.72e+00 1dlyA a.1.1.1 14982 1mqoA 227 6.98e+00 d.157.1.1 103846 1vljA 407 7.42e+00 e.22.1.2 108832 1vl2A 421 7.60e+00 c.26.2.1,d.210.1.1 108708,108709 1x99A 145 8.00e+00 1o8bA 219 8.39e+00 c.124.1.4,d.58.40.1 81180,81181 1q15A 503 8.52e+00 c.26.2.1,d.153.1.1 95538,95539 1s1qA 145 8.59e+00 d.20.1.2 98351 1sr4C 166 8.82e+00 b.42.2.1 105950 1jogA 146 9.54e+00 a.24.16.2 77142 1k66A 149 9.67e+00 c.23.1.1 90941 1umkA 275 9.85e+00 1bqsA 209 1.01e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1f3uA 118 1.03e+01 1f3uA b.65.1.1 27521 1i2aA 219 1.04e+01 e.24.1.1 90660 1h9dB 134 1.05e+01 2jhbA b.54.1.1 60822 1nnxA 109 1.05e+01 b.40.10.1 92013 1fe0A 68 1.09e+01 1cc8A d.58.17.1 39345 1prxA 224 1.10e+01 1prxA c.47.1.10 33076 1iz6A 138 1.18e+01 b.34.5.2,b.40.4.5 76976,76977 1oo0A 147 1.20e+01 d.232.1.1 87182 1js8A 394 1.24e+01 a.86.1.1,b.112.1.1 67219,67220 1cqqA 180 1.24e+01 1cqqA b.47.1.4 26422 1mo9A 523 1.26e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1sv6A 269 1.27e+01 d.177.1.1 106043 1pylA 97 1.28e+01 d.1.1.2 104391 1mxmA 254 1.28e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1r5eA 115 1.29e+01 1ogiA 303 1.34e+01 b.43.4.2,c.25.1.1 92914,92915 2ckiA 262 1.37e+01 1r44A 202 1.43e+01 d.65.1.4 104787 1dbqA 289 1.46e+01 1qpzA c.93.1.1 35666 1br9 194 1.51e+01 1br9 b.40.3.1 25235 1u84A 90 1.52e+01 1rzhM 307 1.53e+01 f.26.1.1 98165 1mngA 203 1.53e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1p1mA 406 1.54e+01 b.92.1.4,c.1.9.9 87696,87697 1tafB 70 1.55e+01 1tafB a.22.1.3 16482 1otgA 125 1.55e+01 1otgA d.80.1.2 39831 1f5jA 199 1.60e+01 1axkA b.29.1.11 24342 1sziA 247 1.62e+01 a.24.23.1 106159 1m3yA 413 1.63e+01 b.121.2.3,b.121.2.3 78579,78580 1x6zA 123 1.65e+01 1qhkA 47 1.76e+01 1qhkA d.100.1.2 40694 1c8uA 285 1.78e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1jhjA 171 1.79e+01 b.18.1.9 66714 1f00I 282 1.81e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1h09A 338 1.81e+01 b.109.1.1,c.1.8.8 83420,83421 1awd 94 1.90e+01 1awd d.15.4.1 37673 1qwkA 317 1.93e+01 c.1.7.1 96482 1ti6B 274 1.97e+01 b.3.5.1,d.58.1.5 106976,106977 1fh0A 221 2.03e+01 1cs8A d.3.1.1 59832 1dkzA 219 2.04e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1rb9 53 2.07e+01 1rb9 g.41.5.1 45214 1npyA 271 2.11e+01 c.2.1.7,c.58.1.5 85995,85996 1alu 186 2.12e+01 1alu a.26.1.1 16826 1cjcA 460 2.14e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1j5pA 253 2.14e+01 d.81.1.3,c.2.1.3 71577,83092 1hf2A 210 2.16e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1gpiA 431 2.19e+01 b.29.1.10 65450 1hfuA 503 2.24e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1ru0A 105 2.25e+01 2nlrA 234 2.26e+01 2nlrA b.29.1.11 24344 1euhA 475 2.27e+01 1euhA c.82.1.1 35369 1j75A 67 2.29e+01 a.4.5.19 62673 1xe7A 203 2.36e+01 1t6cA 315 2.37e+01 c.55.1.8,c.55.1.8 106558,106559 1rzl 91 2.38e+01 1rzl a.52.1.1 17817 1ejxC 567 2.41e+01 b.92.1.1,c.1.9.2 83184,83185 1g8iA 190 2.41e+01 1rec a.39.1.5 60363 1gci 269 2.46e+01 1gci c.41.1.1 32503 1evsA 187 2.46e+01 1evsA a.26.1.1 16845 1mr7A 209 2.47e+01 b.81.1.3 91430 1i5pA 633 2.48e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1ubkL 534 2.51e+01 e.18.1.1 88422 1g5cA 170 2.58e+01 1g5cA c.53.2.1 60264 1pzsA 208 2.60e+01 b.1.8.1 104397 1eueA 86 2.60e+01 1cyo d.120.1.1 59504 1q87A 221 2.62e+01 e.47.1.1 96192 1qwdA 177 2.62e+01 b.60.1.1 96471 1e6yB 433 2.64e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1rjoA 646 2.78e+01 1qipA 183 2.80e+01 1qipA d.32.1.1 38470 1qi9A 556 2.83e+01 1qhbA a.111.1.2 19053 1tmxA 293 2.83e+01 1o5zA 442 2.83e+01 c.59.1.2,c.72.2.2 92530,92531 1avyA 74 2.83e+01 1avyB h.1.17.1 45656 1hekA 131 2.90e+01 a.61.1.5 65818 1l0sA 90 2.95e+01 b.81.2.1 73408 1ryaA 160 2.97e+01 d.113.1.5 105122 1ooyA 481 3.04e+01 c.124.1.3,c.124.1.2 93388,93389 1kpf 126 3.12e+01 1kpf d.13.1.1 37507 1qjtA 99 3.16e+01 1eh2 a.39.1.6 17335 1ofzA 312 3.19e+01 b.68.8.1 86978 1iwmA 186 3.23e+01 b.125.1.2 83758 1m0dA 138 3.25e+01 c.52.1.17 74354 1jjfA 268 3.28e+01 c.69.1.2 66765 1hyoA 421 3.31e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1e1oA 504 3.33e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1go4A 205 3.34e+01 d.135.1.1 70292 1budA 197 3.35e+01 1atlA d.92.1.9 40328 1oq1A 223 3.36e+01 b.29.1.17 93408 1j1nA 492 3.42e+01 c.94.1.1 83978 1h5uA 842 3.63e+01 1a8i c.87.1.4 60655 1f06A 320 3.69e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1jjtA 228 3.71e+01 1a7tA d.157.1.1 63139 1n67A 359 3.79e+01 b.2.3.4,b.2.3.4 85354,85355 1dszB 85 3.87e+01 2nllB g.39.1.2 45108 1usmA 80 3.93e+01 d.74.1.1 99876 1poiA 317 4.12e+01 1poiA c.124.1.2 34153 1m2xA 223 4.12e+01 d.157.1.1 84764 1kjlA 146 4.13e+01 1uwkA 557 4.14e+01 e.51.1.1 108065 1pyoA 167 4.20e+01 c.17.1.1 95370 1dwkA 156 4.24e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1nbwA 607 4.26e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1tq5A 242 4.26e+01 1f08A 148 4.41e+01 1f08A d.89.1.2 59564 1p5zB 263 4.45e+01 c.37.1.1 87815 1h30A 422 4.48e+01 b.29.1.4,b.29.1.4 76604,76605 1ftrA 296 4.50e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1epfA 191 4.51e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1jfrA 262 4.54e+01 1jfrA c.69.1.16 34724 1gkmA 509 4.63e+01 a.127.1.2 70228 1jf9A 408 4.68e+01 1c0nA c.67.1.3 62931 1rm6A 769 4.69e+01 1qfhA 212 4.73e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1jc9A 269 4.79e+01 d.171.1.1 66490 1s1fA 406 4.84e+01 1q5zA 177 4.91e+01 a.196.1.1 95954 1hf8A 289 5.10e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2gf9A 189 5.21e+01 1bdo 80 5.22e+01 1bdo b.84.1.1 28214 1h98A 78 5.22e+01 d.58.1.2 65743 1qfgA 725 5.28e+01 1by5A f.4.3.3 43803 1r69 69 5.37e+01 1r69 a.35.1.2 17028 1avbA 226 5.37e+01 1led b.29.1.1 24158 1ogoX 574 5.46e+01 b.133.1.1,b.80.1.10 92925,92926 1rqpA 299 5.52e+01 b.141.1.1,c.132.1.1 97754,97755 1yfqA 342 5.67e+01 1a91 79 5.67e+01 1a91 f.17.1.1 43635 1w6sA 599 5.68e+01 1vh5A 148 5.71e+01 d.38.1.5 100642 1k8kE 178 5.84e+01 a.148.1.1 68311 1o20A 427 5.89e+01 c.82.1.1 86556 1ejdA 419 5.92e+01 1uae d.68.2.2 39576 1bu6O 501 5.97e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1kxgA 152 5.99e+01 b.22.1.1 73145 1whzA 70 6.02e+01 1ecfA 504 6.04e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1rybA 212 6.05e+01 c.56.3.1 98098 1m1eB 81 6.11e+01 a.161.1.1 78400 1o0iA 138 6.15e+01 d.38.1.5 86532 1lurA 339 6.17e+01 b.30.5.4 84717 1lk5A 229 6.18e+01 c.124.1.4,d.58.40.1 73960,73961 1yc9A 442 6.21e+01 1tukA 67 6.27e+01 1hynP 379 6.29e+01 1hynP d.112.1.2 61408 1jtdB 273 6.30e+01 b.69.5.2 67265 1c7qA 445 6.31e+01 2pgi c.80.1.2 35307 1brfA 53 6.33e+01 1rb9 g.41.5.1 45236 1odkA 235 6.39e+01 c.56.2.1 86863 1kbvA 327 6.40e+01 b.6.1.3,b.6.1.3 68395,68396 1rewC 135 6.60e+01 g.7.1.3 97336 1ms9A 648 6.62e+01 b.29.1.15,b.68.1.1 85088,85089 1ckmA 330 6.64e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1hbnB 442 6.65e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1qwtA 255 6.73e+01 b.26.1.3 96501 1eexA 554 6.73e+01 1dioA c.1.19.3 29650 1q3iA 214 6.80e+01 d.220.1.1 104524 1mqvA 125 6.81e+01 a.24.3.2 79415 1r9hA 135 6.94e+01 d.26.1.1 97260 1exqA 154 7.09e+01 1b9dA c.55.3.2 33646 1fo8A 343 7.09e+01 1foaA c.68.1.10 59927 1ocxA 182 7.09e+01 b.81.1.3 86814 1q1rA 431 7.10e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1c4rA 182 7.12e+01 1c4rA b.29.1.4 24229 1rl0A 255 7.12e+01 1dl5A 317 7.14e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1fi2A 201 7.19e+01 1fi2A b.82.1.2 59845 1jyoA 130 7.21e+01 d.198.1.1 67483 1jb7A 495 7.25e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1jftA 340 7.25e+01 a.35.1.5,c.93.1.1 66652,66653 1gvhA 396 7.31e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1i36A 264 7.35e+01 a.100.1.8,c.2.1.6 71108,71109 1sa3A 262 7.45e+01 c.52.1.23 105400 1xjvA 294 7.48e+01 1pa7A 130 7.66e+01 a.40.1.1 94410 1uebA 184 7.68e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1ouoA 210 7.74e+01 d.4.1.6 93554 1mgrA 99 7.80e+01 d.1.1.2 79106 1wouA 123 7.91e+01 c.47.1.16 109471 1so7A 382 7.91e+01 1czfA 362 7.92e+01 1czfA b.80.1.3 28031 1e42A 258 7.92e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 1odmA 331 7.92e+01 b.82.2.1 86875 1io1A 398 7.99e+01 1io1A e.32.1.1 62611 1pg4A 652 8.00e+01 e.23.1.1 88067 1chmA 401 8.00e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1lniA 96 8.02e+01 d.1.1.2 74046 1k3sA 113 8.16e+01 d.198.1.1 68120 1el6A 219 8.20e+01 1el6B d.182.1.1 42606 1lg7A 182 8.26e+01 d.213.1.1 73888 1iapA 211 8.27e+01 a.91.1.1 62119 1t9bA 677 8.31e+01 1p5dX 463 8.31e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1jb9A 316 8.44e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1jihA 531 8.50e+01 d.240.1.1,e.8.1.7 90374,90375 1n1tA 641 8.51e+01 b.29.1.15,b.68.1.1 79821,79822 1mkmA 249 8.59e+01 a.4.5.33,d.110.2.2 79242,79243 1grj 158 8.65e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1jl0A 334 8.68e+01 1jenA d.156.1.1 63155 2gfaA 119 8.78e+01 1vk1A 242 8.78e+01 d.268.1.2 108634 1jae 471 8.80e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1f3uB 171 8.93e+01 1f3uB b.65.1.1 27525 1j3aA 142 8.95e+01 c.21.1.1 77070 1rzuA 485 8.96e+01 c.87.1.8 105140