# List of top-scoring protein chains for T0303.t04-w0.5 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 1jud 232 5.90e-21 1qq5A c.108.1.1 43325 2ah5A 210 6.46e-21 1zrn 232 6.93e-21 1qq5A c.108.1.1 43323 1te2A 226 2.09e-20 c.108.1.6 106792 2fdrA 229 2.34e-20 2gfhA 260 2.96e-20 1o08A 221 1.50e-19 c.108.1.6 86525 1x42A 232 5.39e-19 1qq5A 253 1.51e-17 1qq5A c.108.1.1 43327 1aq6A 253 1.77e-17 1qq5A c.108.1.1 43331 1rqlA 267 5.57e-17 c.108.1.3 97750 1qq7A 253 5.65e-17 1qq5A c.108.1.1 43329 1fezA 256 9.83e-17 1fezA c.108.1.3 43343 1rdfA 267 1.41e-16 c.108.1.3 104884 1swvA 267 2.21e-16 2fi1A 190 2.74e-14 2b0cA 206 5.67e-13 1l7mA 211 1.89e-11 c.108.1.4 73664 1qyiA 384 2.64e-11 c.108.1.13 96595 1l7pA 211 7.77e-11 c.108.1.4 73670 1j97A 211 7.82e-11 1f5sA c.108.1.4 62753 1zd3A 555 1.58e-10 1cr6A 554 3.42e-10 1cr6B c.69.1.11,c.108.1.2 34687,43337 1vjrA 271 5.45e-10 c.108.1.14 100832 1pw5A 253 2.11e-09 c.108.1.14 95199 1zjjA 263 8.25e-09 1yv9A 264 1.74e-08 1ys9A 254 5.07e-08 2c4nA 250 5.37e-08 1wviA 257 6.51e-08 1ydfA 257 1.38e-07 1nnlA 225 1.04e-06 c.108.1.4 85906 1l8lA 225 1.26e-06 c.108.1.4 84562 1u7pA 164 1.50e-06 1zs9A 261 9.72e-06 2g80A 253 4.23e-05 1wr8A 231 1.03e-04 1yj5A 383 3.96e-04 2b8eA 273 4.42e-04 1rkuA 206 8.61e-04 c.108.1.11 97627 2bdeA 470 9.58e-04 1z5gA 214 1.65e-03 1z88A 214 1.66e-03 2feaA 236 1.94e-03 1ymqA 261 5.65e-03 1nf2A 268 7.53e-03 c.108.1.10 91849 1q92A 197 7.83e-03 c.108.1.8 96250 2b82A 211 7.90e-03 1rmtA 212 7.93e-03 2g09A 297 1.34e-02 2g07A 297 1.54e-02 1k1eA 180 3.40e-02 c.108.1.5 67995 1z4mA 197 3.68e-02 1nrwA 288 4.28e-02 c.108.1.10 86128 2b30A 301 4.74e-02 1rlmA 271 1.05e-01 1wv2A 265 1.22e-01 1hg3A 225 1.52e-01 1hg3A c.1.1.1 61025 1ltqA 301 1.83e-01 c.108.1.9,c.37.1.1 78208,78209 2amyA 246 1.94e-01 1rkqA 282 3.00e-01 c.108.1.10 97621 1rloA 271 4.64e-01 1vctA 205 9.24e-01 1pz1A 333 9.83e-01 c.1.7.1 95390 1pyfA 312 1.37e+00 c.1.7.1 95334 1xviA 275 1.54e+00 1ta0A 197 1.79e+00 c.108.1.16 106729 1t9zA 197 2.05e+00 c.108.1.16 106728 1nb4A 570 2.37e+00 e.8.1.4 85509 1s2oA 244 3.02e+00 1l6rA 227 3.20e+00 c.108.1.10 77768 1ly1A 181 3.33e+00 c.37.1.1 74334 1oc2A 348 3.79e+00 c.2.1.2 92765 1ynpA 317 3.95e+00 1os5A 576 4.34e+00 e.8.1.4 93475 1gx6A 531 4.37e+00 e.8.1.4 70683 1gx5A 536 4.38e+00 e.8.1.4 70682 1csjA 531 4.38e+00 1quvA e.8.1.4 43120 1nhuA 578 4.42e+00 e.8.1.4 85723 1gs5A 258 4.44e+00 c.73.1.2 70395 1quvA 578 4.44e+00 1quvA e.8.1.4 43119 2ax0A 580 4.45e+00 1wzcA 249 4.51e+00 1c2pA 576 4.71e+00 1quvA e.8.1.4 43117 1tj7A 457 4.93e+00 2fueA 262 5.53e+00 1ihiA 323 5.73e+00 c.1.7.1 66142 1j96A 323 5.73e+00 c.1.7.1 71616 1xjbA 325 5.75e+00 1uasA 362 5.84e+00 b.71.1.1,c.1.8.1 88388,88389 1mrqA 323 6.31e+00 c.1.7.1 91445 1q6uA 245 6.75e+00 d.26.1.1 95998 1yvfA 577 7.08e+00 1y8aA 332 7.56e+00 1wpgA 994 7.79e+00 1vbjA 281 9.37e+00 1rjdA 334 1.02e+01 c.66.1.37 97558 1ral 308 1.09e+01 1frb c.1.7.1 28698 1i10A 331 1.10e+01 3ldh c.2.1.5,d.162.1.1 61499,61500 2a72A 146 1.13e+01 1smqA 399 1.16e+01 a.25.1.2 105766 1rjwA 339 1.16e+01 b.35.1.2,c.2.1.1 97582,97583 1jk0A 419 1.17e+01 a.25.1.2 63142 1lwiA 322 1.19e+01 1frb c.1.7.1 28696 1afsA 323 1.19e+01 1frb c.1.7.1 28694 1u02A 239 1.29e+01 c.108.1.15 107538 1x13A 401 1.36e+01 1xpjA 126 1.37e+01 1v6aA 332 1.37e+01 1ry8A 323 1.39e+01 1fjgH 138 1.39e+01 1seiA d.140.1.1 41468 1s1pA 331 1.39e+01 c.1.7.1 98350 1dgsA 667 1.42e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1an7A 136 1.48e+01 1seiA d.140.1.1 41465 1sxeA 97 1.49e+01 a.60.1.1 106080 1e3oC 160 1.65e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1frb 315 1.72e+01 1frb c.1.7.1 28665 1ma3A 253 1.81e+01 c.31.1.5 78883 1c9wA 315 1.99e+01 1frb c.1.7.1 28699 1fehA 574 2.02e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1e08A 371 2.09e+01 i.4.1.1 45914 1bw0A 416 2.19e+01 1bw0A c.67.1.1 34385 2cw1A 65 2.33e+01 1im5A 180 2.47e+01 c.33.1.3 66211 1o1zA 234 2.49e+01 c.1.18.3 86555 1s20A 340 2.64e+01 c.122.1.1 98356 1hfeL 421 2.68e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1i94H 138 2.73e+01 1seiA d.140.1.1 61999 2b8nA 429 2.81e+01 2gd9A 189 2.85e+01 1uekA 275 2.89e+01 d.14.1.5,d.58.26.5 88483,88484 1s05A 129 3.03e+01 a.24.3.2 98254 2fiqA 420 3.05e+01 1qg8A 255 3.05e+01 1qg8A c.68.1.1 34505 1dekA 241 3.11e+01 1dekA c.37.1.1 31842 1tb5A 381 3.12e+01 a.211.1.2 106735 1xm6A 398 3.12e+01 2ctqA 112 3.16e+01 1rtrA 301 3.36e+01 a.128.1.1 97820 1r30A 369 3.37e+01 c.1.28.1 96895 1we5A 772 3.40e+01 2f2hA 773 3.40e+01 1uufA 369 3.41e+01 b.35.1.2,c.2.1.1 100006,100007 1xsjA 778 3.41e+01 1pnuC 197 3.45e+01 i.1.1.1 88200 1vorF 198 3.45e+01 1smaA 588 3.52e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21854,27781,28768 1nwyC 204 3.53e+01 i.1.1.2 86347 1nkwC 205 3.53e+01 i.1.1.2 80588 1rifA 282 3.58e+01 c.37.1.23 97507 1s1mA 545 3.59e+01 c.23.16.1,c.37.1.10 105201,105202 1gviA 588 4.02e+01 b.1.18.2,b.71.1.1,c.1.8.1 70604,70605,70606 1njgA 250 4.11e+01 c.37.1.20 85785 2ldxA 331 4.12e+01 1o69A 394 4.18e+01 c.67.1.4 92560 2gf2A 296 4.23e+01 1wxsA 90 4.24e+01 1bdfA 235 4.24e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1l9uC 1118 4.25e+01 i.8.1.1 73750 1i6vC 1118 4.27e+01 e.29.1.1 61856 1ynjC 1119 4.28e+01 1hqmC 1119 4.30e+01 i.8.1.1 45974 1bcw 319 4.31e+01 1avc a.65.1.1 18176 1j0gA 92 4.35e+01 d.15.1.6 90740 1hzjA 348 4.35e+01 1xel c.2.1.2 61450 1x0lA 333 4.48e+01 1j5wA 298 4.52e+01 d.104.1.1 71589 1e3jA 352 4.54e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1q5mA 322 4.57e+01 c.1.7.1 104539 1q13A 323 4.60e+01 1n44A 319 4.60e+01 a.65.1.1 79980 1noyA 388 4.73e+01 1clqA c.55.3.5 33713 1l7yA 94 4.74e+01 d.15.1.6 73676 1qpwA 141 4.77e+01 1abwA a.1.1.2 15390 2fvlA 324 4.78e+01 1vkmA 297 4.79e+01 c.138.1.1 108670 1ek6A 348 4.82e+01 1xel c.2.1.2 29800 2fliA 220 4.85e+01 4pfk 319 4.90e+01 3pfk c.89.1.1 35582 1losA 224 4.91e+01 c.1.2.3 74157 1i3kA 348 4.94e+01 1xel c.2.1.2 61595 1n42A 319 4.96e+01 a.65.1.1 79979 1cqtA 163 4.97e+01 1au7A a.4.1.1,a.35.1.1 15992,17018 1yacA 208 4.99e+01 1yacA c.33.1.3 31757 1id1A 153 5.03e+01 1id1A c.2.1.9 62286 1klyA 247 5.03e+01 c.1.2.3 72730 1oxy 628 5.17e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18486,18497,21862 2ran 316 5.20e+01 1avc a.65.1.1 18170 1a8b 318 5.25e+01 1avc a.65.1.1 18171 2avyJ 103 5.41e+01 1uz5A 402 5.41e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1hgxA 183 5.42e+01 1tc1A c.61.1.1 34027 1ogqA 313 5.43e+01 c.10.2.8 86996 1n82A 331 5.46e+01 c.1.8.3 91703 1o4xA 167 5.53e+01 a.4.1.1,a.35.1.1 92470,92471 1ll1 628 5.53e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 2bszA 278 5.59e+01 1lla 628 5.60e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1q3kA 259 5.73e+01 c.125.1.1 95693 1ye6A 322 5.73e+01 1bc0 319 5.75e+01 1avc a.65.1.1 18174 1mi3A 322 5.77e+01 c.1.7.1 91274 1n41A 319 5.83e+01 a.65.1.1 79978 2a6hC 1119 5.85e+01 1urhA 280 5.88e+01 c.46.1.2,c.46.1.2 99829,99830 1yj5C 143 5.91e+01 2g8lA 299 5.91e+01 1sm9A 322 5.93e+01 2dldA 337 5.93e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1wyuA 438 5.96e+01 1ujxA 119 5.96e+01 b.26.1.2 99473 2g3mA 693 5.98e+01 1yc5A 246 5.98e+01 1q6hA 224 6.00e+01 d.26.1.1 95975 1z9aA 321 6.00e+01 1ukxA 137 6.06e+01 d.20.1.3 107919 1xxiB 368 6.10e+01 1bc3 319 6.14e+01 1avc a.65.1.1 18175 1nxuA 333 6.15e+01 c.122.1.1 86389 1bcz 319 6.16e+01 1avc a.65.1.1 18177 1jr3A 373 6.17e+01 a.80.1.1,c.37.1.20 63245,63246 2ctwA 109 6.22e+01 1rreA 200 6.27e+01 d.14.1.10 97791 1l9aA 87 6.27e+01 d.201.1.1 73710 1bc1 319 6.37e+01 1avc a.65.1.1 18173 1sjpA 504 6.38e+01 1klzA 247 6.39e+01 c.1.2.3 72731 1jt9A 266 6.40e+01 c.124.1.1 67259 1fs5A 266 6.46e+01 c.124.1.1 65044 1dd9A 338 6.47e+01 1dd9A e.13.1.1 43254 1bcy 319 6.51e+01 1avc a.65.1.1 18172 1eqnA 321 6.66e+01 1dd9A e.13.1.1 43256 2avnA 260 6.76e+01 2genA 197 6.76e+01 1ac5 483 6.77e+01 1ac5 c.69.1.5 34653 1xhkA 187 6.83e+01 1z0sA 278 6.91e+01 2es0A 148 6.93e+01 1tqjA 230 6.94e+01 c.1.2.2 107228 1yjmA 110 6.99e+01 1x94A 191 7.02e+01 c.80.1.3 109522 1mtoA 319 7.11e+01 c.89.1.1 79458 1hyuA 521 7.39e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1oqyA 368 7.42e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1dv7A 227 7.42e+01 1dvjA c.1.2.3 28550 1lngA 87 7.48e+01 d.201.1.1 74045 1lhpA 312 7.50e+01 c.72.1.5 77960 1loqA 228 7.51e+01 c.1.2.3 74155 1suwA 249 7.56e+01 e.52.1.1 106027 1gt0C 159 7.57e+01 a.4.1.1,a.35.1.1 76335,76336 1iq8A 582 7.57e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1te5A 257 7.57e+01 d.153.1.1 106795 1dlaA 314 7.65e+01 1frb c.1.7.1 28690 1ah4 315 7.65e+01 1frb c.1.7.1 28684 1ah0 316 7.66e+01 1frb c.1.7.1 28685 1uok 558 7.70e+01 1uok b.71.1.1,c.1.8.1 27801,28788 6pfkA 319 7.73e+01 3pfk c.89.1.1 35583 1mkp 144 7.75e+01 1vhrA c.45.1.1 32654 1tjnA 156 7.79e+01 c.92.1.3 107048 2bjfA 329 7.82e+01 1j0hA 588 7.91e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1o9gA 250 7.98e+01 c.66.1.29 86692 1r38A 322 8.02e+01 1tiiA 190 8.07e+01 1lt3A d.166.1.1 42238 1dgwY 93 8.10e+01 1caxB 1kd6A 179 8.11e+01 b.97.1.1 68459 1iazA 179 8.13e+01 1iazA b.97.1.1 62131 1dvjA 246 8.20e+01 1dvjA c.1.2.3 28546 1v2aA 210 8.20e+01 a.45.1.1,c.47.1.5 100263,100264 1us5A 314 8.21e+01 c.94.1.1 99856 1nndA 255 8.22e+01 e.8.1.2 92002 1vp8A 201 8.22e+01 1s1hH 129 8.33e+01 i.1.1.1 105160 1dcnA 433 8.37e+01 1auwA a.127.1.1 19420 1qhdA 398 8.54e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1l1jA 239 8.61e+01 b.47.1.1 84516 1dcnD 445 8.62e+01 1auwA a.127.1.1 19423 1j0jA 588 8.63e+01 b.1.18.2,b.71.1.1,c.1.8.1 77039,77040,77041 1dcnC 447 8.69e+01 1auwA a.127.1.1 19422 1twuA 139 8.70e+01 d.32.1.8 107413 1gwyA 175 8.79e+01 b.97.1.1 83356 1km3A 247 8.80e+01 c.1.2.3 72739 1o9hA 250 8.85e+01 c.66.1.29 86693 1t2fA 333 8.89e+01 c.2.1.5,d.162.1.1 99088,99089 1x1zA 252 8.93e+01