# List of top-scoring protein chains for t04-100-30-dssp-ebghstl-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 2cw8A 537 4.75e-01 1mjc 69 5.87e-01 1mjc b.40.4.5 25319 1wkaA 147 8.73e-01 1vdwA 254 1.69e+00 e.7.1.1 100569 1q8rA 120 1.92e+00 d.79.6.1 96225 1vjvA 415 2.72e+00 d.3.1.9 108632 1lshA 1056 2.94e+00 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1mwmA 320 2.98e+00 c.55.1.1,c.55.1.1 79580,79581 2fdiA 211 3.06e+00 1bf2 750 4.01e+00 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1t9fA 187 4.05e+00 b.42.6.1 106710 1xwvA 129 4.48e+00 1bzyA 217 5.11e+00 1qk3A c.61.1.1 34071 1vjlA 164 6.12e+00 d.257.1.1 100822 2fsrA 195 6.24e+00 1eu3A 210 6.55e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1khoA 370 6.75e+00 a.124.1.1,b.12.1.3 72489,72490 1ev7A 317 7.59e+00 1ev7B c.52.1.9 33315 1v88A 130 7.88e+00 b.55.1.1 108423 2fpeA 62 8.34e+00 1z7gA 217 8.40e+00 1jsdA 319 8.40e+00 b.19.1.2 63258 1ze3D 125 8.48e+00 3tss 194 8.63e+00 1aw7A b.40.2.2,d.15.6.1 25160,37749 1snrA 341 8.89e+00 b.6.1.3,b.6.1.3 105823,105824 1j9qA 341 8.96e+00 1nif b.6.1.3,b.6.1.3 62765,62766 1wm5A 208 9.07e+00 1hh8A 213 9.14e+00 1e96B a.118.8.1 61042 1nekA 588 9.17e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1xn5A 146 9.44e+00 1yt5A 258 9.55e+00 1tdhA 364 9.83e+00 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1b0uA 262 9.87e+00 1b0uA c.37.1.12 32370 1dkuA 317 9.92e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1sawA 225 9.96e+00 1c9oA 66 1.02e+01 1mjc b.40.4.5 25325 1zk7A 467 1.05e+01 1jsmA 325 1.07e+01 b.19.1.2 63264 1uliA 460 1.18e+01 b.33.1.2,d.129.3.3 107921,107922 2gfaA 119 1.22e+01 1zkpA 268 1.23e+01 1dgwA 178 1.25e+01 1dgwA b.82.1.2 28090 1gt91 357 1.27e+01 1t1gA 364 1.28e+01 c.41.1.2 106246 1vhsA 175 1.28e+01 d.108.1.1 100698 1aw7A 194 1.29e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1ktjA 129 1.32e+01 b.1.18.7 72974 1yfsA 465 1.34e+01 1fjgK 129 1.34e+01 1fjfK c.55.4.1 33733 1sf9A 128 1.39e+01 b.34.15.1 98831 1fjrA 195 1.39e+01 1fjrA b.102.1.1 59855 1riqA 465 1.41e+01 a.203.1.1,d.104.1.1 97516,97517 1qhxA 178 1.41e+01 1qhsA c.37.1.3 31936 1tl2A 236 1.42e+01 1tl2A b.67.1.1 27541 1d4tA 104 1.47e+01 1d4tA d.93.1.1 40537 1nnxA 109 1.48e+01 b.40.10.1 92013 1q38A 89 1.50e+01 b.1.2.1 95663 2bbvA 363 1.50e+01 2bbvA b.121.4.4 23323 1cseE 274 1.55e+01 1gci c.41.1.1 32481 2f9nA 245 1.56e+01 1lw6E 281 1.56e+01 c.41.1.1 74293 1sup 275 1.58e+01 1gci c.41.1.1 32510 1wkrA 340 1.59e+01 b.50.1.2 109395 1sgt 223 1.60e+01 5ptp b.47.1.1 25814 1os8A 223 1.61e+01 b.47.1.1 93481 1eg9A 449 1.61e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1lr7A 74 1.62e+01 g.3.11.3,g.68.1.1 84679,84680 1c5yB 253 1.62e+01 5ptp 1o7nA 449 1.63e+01 b.33.1.2,d.129.3.3 81162,81163 1to2E 281 1.64e+01 1vkyA 347 1.64e+01 e.53.1.1 108696 1g4mA 393 1.71e+01 b.1.18.11,b.1.18.11 65143,65144 1c8uA 285 1.72e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1cf1A 404 1.78e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 2viuA 328 1.81e+01 1hgeA b.19.1.2 23797 1jnuA 104 1.90e+01 d.110.3.6 71762 1gj7B 253 2.01e+01 1tygB 87 2.09e+01 d.15.3.2 107455 1go7P 462 2.11e+01 b.80.7.1,d.92.1.6 76245,76246 1i8kA 107 2.14e+01 b.1.1.1 71130 1txqA 93 2.15e+01 1vqoU 66 2.16e+01 1yifA 533 2.18e+01 1jovA 270 2.19e+01 b.30.5.7 84192 1mojA 182 2.19e+01 a.25.1.1 91367 1tjoA 182 2.19e+01 1inlA 296 2.21e+01 c.66.1.17 66220 1l1jA 239 2.21e+01 b.47.1.1 84516 1k7iA 479 2.22e+01 b.80.7.1,d.92.1.6 77281,77282 1h2wA 710 2.23e+01 b.69.7.1,c.69.1.4 76596,76597 1wdtA 665 2.24e+01 1vr9A 213 2.25e+01 1i8aA 189 2.27e+01 1i82A b.1.9.2 61951 1y1oA 203 2.27e+01 1zxiC 288 2.28e+01 1ee6A 197 2.28e+01 1ee6A b.80.1.1 28024 1zxiF 288 2.31e+01 1p8xA 344 2.33e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 2f4qA 346 2.34e+01 1wwzA 159 2.40e+01 1o6aA 96 2.45e+01 b.139.1.1 92562 1s8iA 121 2.48e+01 a.133.1.2 98735 1svy 114 2.49e+01 1svy d.109.1.1 40831 2mcm 112 2.50e+01 2mcm b.1.7.1 22207 1t92A 116 2.52e+01 1lxiA 139 2.53e+01 g.17.1.2 84735 2b1xA 470 2.58e+01 1vdxA 184 2.60e+01 3c2c 112 2.63e+01 1ycc a.3.1.1 15885 1vplA 256 2.70e+01 2fikA 287 2.74e+01 2cxaA 256 2.74e+01 1mzyA 333 2.76e+01 b.6.1.3,b.6.1.3 103848,103849 1b12A 248 2.76e+01 1b12A b.87.1.2 28388 1wyxA 69 2.87e+01 1wjnA 97 2.88e+01 1n7oA 721 2.92e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1f53A 84 2.94e+01 1f53A b.11.1.4 23632 1a8q 274 3.01e+01 1brt c.69.1.12 34702 1c1yB 77 3.07e+01 1c1yB d.15.1.5 37618 1dwkA 156 3.08e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1nz0A 118 3.11e+01 d.14.1.2 86433 1geeA 261 3.14e+01 c.2.1.2 90509 1gcoA 261 3.18e+01 1ybvA c.2.1.2 29884 2fp7A 54 3.18e+01 1yb3A 175 3.44e+01 1vbkA 307 3.49e+01 1y4lA 121 3.51e+01 2anwA 241 3.51e+01 1jb0D 138 3.53e+01 1jb0D d.187.1.1 62823 1hbq 183 3.55e+01 1aqb b.60.1.1 27078 1k3sA 113 3.56e+01 d.198.1.1 68120 1n62C 288 3.57e+01 d.87.2.1,d.145.1.3 80094,80095 1d9tA 289 3.59e+01 1deaA 1o0pA 104 3.61e+01 d.58.7.1 86535 1ltoA 245 3.65e+01 b.47.1.2 84707 1hg8A 349 3.67e+01 b.80.1.3 65830 1hkyA 86 3.71e+01 g.10.1.3 76714 1el6A 219 3.73e+01 1el6B d.182.1.1 42606 1u2xA 474 3.73e+01 c.72.1.3 107622 1vgjA 184 3.74e+01 1f35A 162 3.76e+01 1f35A b.94.1.1 59628 1y88A 199 3.78e+01 1ahsA 126 3.80e+01 1ahsA b.19.1.1 23794 1e79H 146 3.81e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1ne7A 289 3.81e+01 c.124.1.1 91833 1iw8A 231 3.87e+01 a.111.1.1 76866 1zvkA 358 3.87e+01 1gy7A 125 3.92e+01 d.17.4.2 70738 2a72A 146 3.95e+01 1qfmA 710 3.96e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1gycA 499 4.07e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1d2tA 231 4.09e+01 1d2tA a.111.1.1 19052 1k3bA 119 4.10e+01 b.61.5.1 72016 1bywA 110 4.15e+01 1bywA d.110.3.6 40912 2g0cA 76 4.15e+01 1ojxA 263 4.16e+01 c.1.10.1 93164 1tlyA 278 4.17e+01 f.4.6.1 107143 2anyA 241 4.17e+01 1rqpA 299 4.28e+01 b.141.1.1,c.132.1.1 97754,97755 1w8sA 263 4.29e+01 2aexA 346 4.31e+01 1kv7A 488 4.32e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 2bwqA 129 4.33e+01 1vi4A 174 4.34e+01 c.8.7.1 100731 1c7sA 858 4.39e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1udzA 182 4.40e+01 b.51.1.1 99239 1wruA 379 4.42e+01 1qj2C 285 4.45e+01 1qj2C 1krhA 338 4.46e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1pv5A 264 4.47e+01 d.251.1.1 95150 1ts9A 102 4.48e+01 1kcqA 104 4.54e+01 d.109.1.1 68449 1bia 321 4.54e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1o0wA 252 4.55e+01 a.149.1.1,d.50.1.1 80751,80752 1php 394 4.57e+01 16pk c.86.1.1 35452 1rm6A 769 4.64e+01 1uc2A 481 4.66e+01 d.261.1.1 99161 1sqhA 312 4.66e+01 d.108.1.5 98966 1kqfC 217 4.71e+01 f.21.1.1 72874 1hx0A 496 4.75e+01 b.71.1.1,c.1.8.1 61346,61347 1ppa 121 4.77e+01 1poa a.133.1.2 19550 1vr3A 191 4.77e+01 1cv8 174 4.80e+01 1cv8 d.3.1.1 37089 1y4wA 518 4.87e+01 1yg9A 330 4.87e+01 1zq7A 207 4.88e+01 1mr1C 99 4.91e+01 d.217.1.2 79420 2bs9A 503 4.91e+01 2akrA 285 4.97e+01 1u9cA 224 4.98e+01 1xf1A 926 5.00e+01 1wk8A 194 5.00e+01 1r0rE 274 5.01e+01 c.41.1.1 96735 1yqtA 538 5.01e+01 1dg6A 191 5.09e+01 1d4vB b.22.1.1 23883 2bfgA 503 5.14e+01 1yu6A 275 5.14e+01 1whzA 70 5.16e+01 1o4tA 133 5.17e+01 b.82.1.9 86622 1rl6A 177 5.23e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 2bhgA 209 5.24e+01 1rds 105 5.26e+01 9rnt d.1.1.4 36236 1wosA 364 5.28e+01 b.44.2.1,d.250.1.1 109468,109469 1sv6A 269 5.28e+01 d.177.1.1 106043 1zbqA 327 5.34e+01 1eguA 731 5.34e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 2fv7A 331 5.36e+01 1xxsA 122 5.37e+01 1xewX 182 5.38e+01 1i31A 314 5.40e+01 1bw8A b.2.7.1 22481 1xttA 216 5.46e+01 1yhtA 367 5.47e+01 1qipA 183 5.52e+01 1qipA d.32.1.1 38470 1qwzA 235 5.54e+01 b.100.1.1 96510 1l1oC 181 5.57e+01 b.40.4.3 73480 1z64A 26 5.58e+01 1v8bA 479 5.60e+01 1op3H 225 5.61e+01 b.1.1.1,b.1.1.2 87208,87209 2bmoA 447 5.62e+01 1xovA 326 5.65e+01 1vj0A 380 5.68e+01 b.35.1.2,c.2.1.1 100786,100787 2bklA 695 5.75e+01 1h8eH 146 5.76e+01 1e79H b.93.1.1 60757 1cm9A 74 5.77e+01 1b3aA d.9.1.1 37405 1mbyA 88 5.81e+01 d.223.1.1 78931 1msk 331 5.83e+01 1msk d.173.1.1 42495 4ubpA 101 5.84e+01 1ubpA d.8.1.1 37352 1ro7A 259 5.86e+01 c.130.1.1 97667 1fm2B 520 5.88e+01 1fm2B 1fyhB 229 5.88e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1q6uA 245 5.97e+01 d.26.1.1 95998 1wr7A 41 6.00e+01 1zxtA 76 6.01e+01 1ri9A 102 6.01e+01 b.34.2.1 97506 1jj2T 66 6.05e+01 1ffkR g.39.1.6 63105 1s72U 66 6.05e+01 g.39.1.6 105340 1fnlA 175 6.08e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1wpuA 147 6.10e+01 1u79A 129 6.11e+01 d.26.1.1 107714 1wmqA 147 6.12e+01 1pkoA 139 6.16e+01 b.1.1.1 88147 1v6pA 62 6.18e+01 1yoyA 175 6.20e+01 1p42A 270 6.24e+01 d.14.1.7,d.14.1.7 87754,87755 4dpvZ 584 6.28e+01 2cas b.121.5.2 23377 1wggA 96 6.29e+01 1jj2R 84 6.32e+01 1ffkP d.12.1.1 63103 1v5tA 90 6.35e+01 d.15.1.1 108385 2fbwA 621 6.37e+01 1s72S 85 6.40e+01 d.12.1.1 105338 1ji6A 589 6.43e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1nziA 159 6.44e+01 b.23.1.1,g.3.11.1 86449,86450 1hpi 71 6.44e+01 1ckuA g.35.1.1 44995 1yx1A 264 6.48e+01 1se8A 301 6.50e+01 b.40.4.3 105448 1wsrA 375 6.50e+01 1k8kD 300 6.50e+01 d.198.2.1,d.198.2.1 68309,68310 1dkgA 197 6.55e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1t0gA 109 6.61e+01 d.120.1.2 99063 1vqoS 85 6.62e+01 1sh7A 284 6.64e+01 1o12A 376 6.68e+01 b.92.1.5,c.1.9.10 80758,80759 1umzA 278 6.72e+01 b.29.1.2 99639 1ad2 228 6.85e+01 1ad2 e.24.1.1 43353 2ae5B 528 6.86e+01 1qi9A 556 6.91e+01 1qhbA a.111.1.2 19053 2gd9A 189 6.98e+01 2gxfA 142 6.99e+01 1fsgA 233 7.00e+01 1qk3A c.61.1.1 34029 1nif 340 7.00e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1yozA 116 7.06e+01 2fl4A 149 7.08e+01 1nr4A 71 7.08e+01 d.9.1.1 92077 1mfgA 95 7.08e+01 b.36.1.1 79043 1yavA 159 7.16e+01 1o54A 277 7.28e+01 c.66.1.13 92482 1kcbA 340 7.39e+01 b.6.1.3,b.6.1.3 90951,90952 1ruwA 69 7.42e+01 2bw4A 340 7.51e+01 1pqxA 91 7.52e+01 d.267.1.1 104296 1rzfH 235 7.62e+01 b.1.1.1,b.1.1.2 98150,98151 1ikpA 613 7.62e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1v5vA 401 7.65e+01 1uscA 178 7.71e+01 b.45.1.2 99860 1tg0A 68 7.71e+01 1jyhA 157 7.78e+01 d.60.1.3 71956 1juvA 193 7.84e+01 c.71.1.1 90912 1r4pB 70 7.92e+01 b.40.2.1 97026 1wnyA 186 7.93e+01 1z5bA 469 7.95e+01 1wxcB 134 7.96e+01 1l7lA 121 7.97e+01 b.18.1.16 77790 1tkiA 321 7.98e+01 1tkiA d.144.1.7 41638 1pne 140 8.14e+01 1pne d.110.1.1 40866 2bmoB 194 8.16e+01 1rc6A 261 8.16e+01 b.82.1.11 97287 2ai4A 119 8.17e+01 1oruA 195 8.23e+01 b.58.1.2 93464 1xm0A 147 8.23e+01 1n9eA 787 8.26e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 2f4pA 147 8.27e+01 1jnrA 643 8.28e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1l3pA 102 8.38e+01 a.24.17.1 84520 1w66A 232 8.45e+01 2a6zA 222 8.45e+01 2ff4A 388 8.48e+01 1qwrA 319 8.65e+01 b.82.1.3 96491 2adgA 214 8.67e+01 1m4iA 181 8.68e+01 d.108.1.1 74457 2fhpA 187 8.69e+01 2c43A 323 8.74e+01 1mgrA 99 8.81e+01 d.1.1.2 79106 2evbA 74 8.84e+01 1vgwA 231 8.88e+01 c.68.1.13 100612 1ca1 370 8.89e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 2fbyA 205 8.90e+01 1zzcA 198 8.90e+01 1k2xB 143 8.91e+01 1eaiC 61 8.91e+01 1eaiC g.22.1.1 44894 1wdxA 69 8.97e+01 1g0hA 252 8.98e+01 1dk4A e.7.1.1 60171 1f39A 101 9.00e+01 1umuA b.87.1.1 28386