# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 1s5uA 138 4.93e-14 d.38.1.1 98573 2cyeA 133 1.61e-13 1z54A 132 2.43e-13 2gf6A 135 2.44e-12 2av9A 147 3.01e-12 1njkA 156 4.03e-12 d.38.1.1 85818 2essA 248 2.26e-11 2aliA 158 3.02e-11 1lo7A 141 3.32e-11 d.38.1.1 74144 1bvqA 141 9.47e-11 1bvqA d.38.1.1 38542 1vpmA 169 4.58e-10 1yliA 153 1.25e-09 2h4uA 145 2.75e-08 1wluA 136 7.61e-08 1j1yA 136 7.76e-08 d.38.1.5 90776 2cwzA 141 9.93e-08 1psuA 140 2.64e-07 d.38.1.5 88285 2fs2A 151 2.84e-07 2b6eA 146 4.26e-07 2gvhA 288 4.40e-07 1u1zA 168 4.89e-07 d.38.1.6 107602 1zkiA 133 6.54e-07 1ixlA 131 6.83e-07 d.38.1.5 90717 1o0iA 138 8.04e-07 d.38.1.5 86532 1vh5A 148 1.18e-06 d.38.1.5 100642 1z6bA 154 2.07e-06 1q4uA 151 3.79e-06 d.38.1.5 95828 2b3nA 159 1.87e-05 1yocA 147 1.47e-04 1t82A 155 1.75e-04 d.38.1.5 106639 1c8uA 285 2.26e-04 1c8uA d.38.1.3,d.38.1.3 38547,38548 1tbuA 118 2.84e-04 1iq6A 134 7.97e-04 d.38.1.4 76755 1mkaA 171 8.83e-04 1mkaA d.38.1.2 38543 2bi0A 337 1.02e-03 1sh8A 154 2.87e-03 d.38.1.5 105549 1pn2A 280 3.82e-02 d.38.1.4,d.38.1.4 94930,94931 1nbwA 607 6.77e-02 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1kk1A 410 1.16e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1jnyA 435 1.18e-01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1jv4A 162 1.52e-01 b.60.1.1 67343 1fmtA 314 1.67e-01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1xyiA 66 1.91e-01 2d0oA 610 1.95e-01 1koiA 184 1.97e-01 b.60.1.1 68725 1wdeA 294 1.99e-01 2as9A 210 2.09e-01 1ha3A 405 2.15e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2df7A 458 2.45e-01 1qy1A 174 2.57e-01 b.60.1.1 96568 1i05A 180 2.91e-01 1mup b.60.1.1 27130 1sy3A 184 3.04e-01 b.60.1.1 106110 1j48A 110 3.12e-01 b.1.7.1 84112 1i06A 180 3.70e-01 1mup b.60.1.1 27131 2fauA 341 4.01e-01 1qy6A 274 4.37e-01 b.47.1.1 96574 1erxA 184 4.55e-01 1np1A b.60.1.1 27164 1pm1X 180 4.60e-01 b.60.1.1 104189 1sv6A 269 4.65e-01 d.177.1.1 106043 1ynmA 247 5.35e-01 1mup 166 5.51e-01 1mup b.60.1.1 27133 1peeA 180 5.54e-01 b.60.1.1 104126 1x89A 178 5.57e-01 1gpmA 525 6.51e-01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1azpA 66 6.52e-01 1azpA b.34.13.1 37467 1m1hA 248 6.64e-01 b.114.1.1,d.58.42.1 78415,78416 1ja1A 622 6.69e-01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1zndA 174 7.51e-01 1noa 113 8.67e-01 2mcm b.1.7.1 22208 2a19A 175 8.74e-01 2d1eA 248 9.16e-01 1x71A 178 9.17e-01 1s0uA 408 9.56e-01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1th0A 226 1.02e+00 d.3.1.7 106903 1dzkA 157 1.02e+00 1obpA b.60.1.1 27096 1fm0E 150 1.03e+00 1fmaE d.41.5.1 38629 1obpA 159 1.06e+00 1obpA b.60.1.1 27092 1wcdJ 441 1.08e+00 1euoA 180 1.18e+00 1np1A b.60.1.1 27163 1f60A 458 1.20e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1exmA 405 1.22e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2c78A 405 1.29e+00 2mcm 112 1.37e+00 2mcm b.1.7.1 22207 2gfgA 193 1.41e+00 1q8rA 120 1.45e+00 d.79.6.1 96225 1bj7 156 1.51e+00 1bj7 b.60.1.1 27113 1tllA 688 1.56e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1hn2A 159 1.57e+00 b.60.1.1 65890 2cw5A 255 1.66e+00 1umgA 362 1.74e+00 d.280.1.1 107956 1f3mA 80 1.81e+00 1f3mA j.66.1.1 46358 1wosA 364 1.83e+00 b.44.2.1,d.250.1.1 109468,109469 2fi9A 128 1.85e+00 1zboA 210 1.88e+00 1w1wA 430 1.88e+00 1xbrA 184 1.89e+00 1xbrA b.2.5.4 22458 1gt1A 159 1.90e+00 b.60.1.1 90515 1wj9A 211 1.95e+00 1f39A 101 2.00e+00 1umuA b.87.1.1 28386 1tw0A 157 2.02e+00 1n4xH 120 2.04e+00 b.1.1.1 85324 1jzuA 157 2.06e+00 b.60.1.1 84271 1d2eA 397 2.09e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1kcxA 518 2.10e+00 b.92.1.3,c.1.9.6 90953,90954 1is1A 185 2.14e+00 d.67.3.1 83704 1mbyA 88 2.26e+00 d.223.1.1 78931 1eq6A 189 2.29e+00 1eq6A d.107.1.1 40796 2fkcA 247 2.33e+00 1hdmB 193 2.38e+00 1hdmB b.1.1.2,d.19.1.1 21584,38158 1gvzA 237 2.43e+00 b.47.1.2 76360 1v7lA 163 2.46e+00 1kl9A 182 2.50e+00 b.40.4.5 72681 1e5pA 151 2.52e+00 1bj7 b.60.1.1 59272 1vrmA 325 2.55e+00 1x8qA 184 2.56e+00 1lf7A 182 2.58e+00 b.60.1.1 73878 1zwyA 185 2.59e+00 1w9yA 319 2.76e+00 1iznA 286 2.77e+00 e.43.1.1 83847 1go4A 205 2.81e+00 d.135.1.1 70292 1mqkH 127 2.84e+00 b.1.1.1 85053 2as0A 396 2.85e+00 1lla 628 2.90e+00 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1rg9A 383 2.91e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1iz6A 138 2.98e+00 b.34.5.2,b.40.4.5 76976,76977 1fu1A 203 2.99e+00 1fu1B b.59.1.1,h.1.11.1 27076,45630 1howA 373 3.04e+00 1hcl d.144.1.7 41679 1a2yB 116 3.06e+00 1gc1H b.1.1.1 19927 1e2wA 251 3.08e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 1ywsA 82 3.14e+00 2eifA 136 3.14e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1y96A 86 3.15e+00 1ymqA 261 3.17e+00 1zvhA 134 3.21e+00 1lldA 319 3.24e+00 3ldh c.2.1.5,d.162.1.1 30177,42144 1wwbX 103 3.26e+00 1wwcA b.1.1.4 21777 1ihnA 113 3.37e+00 1ihnA c.103.1.1 62388 2prd 174 3.41e+00 2prd b.40.5.1 25435 1y8oA 419 3.41e+00 1spjA 238 3.43e+00 1jhsA 188 3.49e+00 d.107.1.1 84172 2glzA 153 3.58e+00 1a49A 530 3.64e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1ol0A 121 3.76e+00 b.1.1.1 93296 1c8cA 64 3.78e+00 1azpA b.34.13.1 59084 1fiqB 350 3.87e+00 1fiqB d.87.2.1,d.145.1.3 40229,41760 1xfpA 142 3.90e+00 b.1.1.1 109587 1tyjA 170 3.92e+00 1zy1B 197 3.94e+00 1bkb 136 3.94e+00 1bkb b.34.5.2,b.40.4.5 24609,25341 1oaqH 121 3.96e+00 b.1.1.1 92707 1lj5A 379 4.06e+00 e.1.1.1 73928 1vcaA 202 4.09e+00 1vcaA b.1.1.3,b.1.1.4 21649,21685 1jhfA 202 4.17e+00 a.4.5.2,b.87.1.1 63057,63058 1fuiA 591 4.25e+00 1fuiA b.43.2.1,c.85.1.1 25674,35444 2ftwA 521 4.34e+00 2bzpA 226 4.38e+00 2g50A 530 4.39e+00 1jmmA 377 4.40e+00 b.30.6.1 71749 2btiA 63 4.44e+00 1x6oA 174 4.49e+00 b.34.5.2,b.40.4.5 109493,109494 1b7yA 350 4.58e+00 1pysA d.104.1.1 40776 1q3iA 214 4.58e+00 d.220.1.1 104524 1g5hA 454 4.65e+00 1g5hA c.51.1.1,d.104.1.1 60270,60271 1amuA 563 4.65e+00 1amuA e.23.1.1 43351 1u2kA 309 4.71e+00 2bm3A 166 4.78e+00 1f8rA 498 4.78e+00 1f8rA c.3.1.2,d.16.1.5 30410,37974 1a6wH 120 4.82e+00 1mfa b.1.1.1 20253 1j1qA 261 4.83e+00 d.165.1.1 90768 1brwA 433 4.86e+00 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2blnA 305 4.86e+00 1sek 378 4.87e+00 1sek e.1.1.1 42675 2c7hA 86 4.92e+00 1qm4A 396 4.95e+00 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1g7sA 594 4.98e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1vqoH 171 5.02e+00 1jvwA 167 5.04e+00 d.26.1.1 71907 2gfaA 119 5.10e+00 1wucA 250 5.13e+00 1nstA 325 5.21e+00 1nstA c.37.1.5 31951 2a8jA 420 5.22e+00 1khiA 176 5.24e+00 b.34.5.2,b.40.4.5 77408,77409 2bszA 278 5.35e+00 1g87A 614 5.49e+00 a.102.1.2,b.2.2.2 83275,83276 2apxA 112 5.53e+00 1mtpA 323 5.53e+00 e.1.1.1 85107 1qqsA 174 5.54e+00 1nglA b.60.1.1 27143 1eaf 243 5.60e+00 1eaf c.43.1.1 32617 2gjgA 248 5.60e+00 1txqA 93 5.70e+00 1g7nA 131 5.75e+00 b.60.1.2 83274 1xqbA 247 5.75e+00 1f8vA 355 5.78e+00 2bbvA b.121.4.4 23329 1bza 262 5.83e+00 1btl e.3.1.1 42701 1q8yA 373 5.86e+00 d.144.1.7 96234 2bnmA 198 5.93e+00 1tvgA 153 5.94e+00 2cyjA 118 5.98e+00 1j5uA 136 6.05e+00 d.208.1.1 71584 1vemA 516 6.06e+00 2a8mA 420 6.07e+00 1vqoR 155 6.10e+00 2breA 219 6.15e+00 1i7oA 429 6.19e+00 1i7oA d.177.1.1,d.177.1.1 61893,61894 1el6A 219 6.23e+00 1el6B d.182.1.1 42606 1gttA 429 6.25e+00 d.177.1.1,d.177.1.1 70529,70530 1lfo 128 6.48e+00 1hmt b.60.1.2 27223 1dceA 567 6.49e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1t2jA 116 6.49e+00 1s72H 171 6.57e+00 d.41.4.1 105327 1qr0A 228 6.62e+00 1qr0A d.150.1.1,d.150.1.1 59038,59039 1uwvA 433 6.67e+00 b.40.4.12,c.66.1.40 100128,100129 1d5tA 433 6.70e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1aihA 170 6.80e+00 1aihA d.163.1.1 42149 1a34A 159 6.82e+00 1a34A b.121.7.1 23286 1amy 403 6.85e+00 1jdc b.71.1.1,c.1.8.1 27799,28786 1wbpA 397 6.87e+00 1k7hA 476 6.88e+00 c.76.1.1 72101 1sczA 233 6.90e+00 c.43.1.1 98802 1rypB 250 6.91e+00 1rypB d.153.1.4 41933 1nbfD 76 6.93e+00 d.15.1.1 80390 1acf 125 6.93e+00 3nul d.110.1.1 40882 1yqyA 523 6.98e+00 1in0A 163 7.01e+00 d.58.49.1,d.58.49.1 83694,83695 1r9wA 145 7.05e+00 d.89.1.2 97264 1j05B 121 7.14e+00 b.1.1.1 90736 1vyfA 135 7.14e+00 b.60.1.2 108902 1d7yA 408 7.31e+00 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2a9kB 223 7.34e+00 1gp6A 356 7.47e+00 b.82.2.1 65441 1u14A 172 7.48e+00 c.51.4.3 107579 2ccvA 101 7.61e+00 2btzA 394 7.64e+00 1zyeA 220 7.64e+00 1t4wA 196 7.66e+00 b.2.5.2 106427 1gpc 218 7.80e+00 1gpc b.40.4.7 25393 1qhlA 227 7.81e+00 1qhlA c.37.1.12 32382 1g7jA 107 7.83e+00 32c2A b.1.1.1 19932 1uscA 178 7.87e+00 b.45.1.2 99860 2bc4A 211 7.88e+00 1qciA 262 7.93e+00 1qi7A d.165.1.1 42201 1at0 145 7.99e+00 1at0 b.86.1.1 28374 1wmhA 89 8.02e+00 1xkiA 162 8.03e+00 1lid 131 8.06e+00 1hmt b.60.1.2 27184 1nxzA 246 8.16e+00 b.122.1.2,c.116.1.5 86391,86392 1o6uA 403 8.20e+00 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1wgvA 124 8.24e+00 830cA 168 8.26e+00 1ck7A d.92.1.11 40400 1ncwH 222 8.30e+00 b.1.1.1,b.1.1.2 85555,85556 1bt0A 76 8.32e+00 1ubi d.15.1.1 37607 1lfpA 249 8.33e+00 e.39.1.1 73885 1l2hA 153 8.33e+00 b.42.1.2 77655 1bebA 162 8.35e+00 1bebA b.60.1.1 27115 1fthA 122 8.37e+00 d.150.1.2 60028 2sak 121 8.38e+00 2sak d.15.5.1 37711 1mvuB 121 8.59e+00 b.1.1.1 91475 1pcfA 66 8.60e+00 1pcfA d.18.1.1 38142 1f5mA 180 8.67e+00 1f5mB d.110.2.1 40895 2fytA 340 8.69e+00 1vkjA 285 8.72e+00 c.37.1.5 108666 1zxzA 197 8.75e+00 1a7qL 106 8.83e+00 8fabA b.1.1.1 19954 1pysA 350 8.95e+00 1pysA d.104.1.1 40775 1je6A 275 8.96e+00 b.1.1.2,d.19.1.1 71638,71639 1a2yA 107 9.01e+00 8fabA b.1.1.1 19926 1l8rA 101 9.02e+00 a.6.1.4 73700 1gz8A 299 9.08e+00 d.144.1.7 83405 1efpB 252 9.09e+00 1efvB c.26.2.3 31636 1vpzA 73 9.12e+00 1u0kA 288 9.14e+00 d.21.1.2,d.21.1.2 107547,107548 1f97A 212 9.15e+00 1f97A b.1.1.1,b.1.1.4 19763,21764 1omhA 293 9.30e+00 d.89.1.5 93348 1hdmA 201 9.46e+00 1iakA b.1.1.2,d.19.1.1 21583,38157 3il8 72 9.49e+00 1tvxA d.9.1.1 37356 1uz5A 402 9.49e+00 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1lfdA 87 9.49e+00 1lfdA d.15.1.5 37622 2bpa1 426 9.58e+00 2bpa1 1y7mA 164 9.63e+00 1vhyA 257 9.64e+00 b.122.1.2,c.116.1.5 100714,100715 1yzbA 182 9.69e+00 2gupA 292 9.72e+00 1tvxA 75 9.73e+00 1tvxA d.9.1.1 37441 1ogwA 76 9.80e+00 d.15.1.1 87001 1zsqA 528 9.96e+00 1hx6A 394 9.98e+00 1cjdA b.121.2.1,b.121.2.1 58995,58996 1sc6A 404 1.02e+01 1flmA 122 1.03e+01 1axj b.45.1.1 25747 1ktjA 129 1.03e+01 b.1.18.7 72974 1j1lA 290 1.03e+01 b.82.1.12 90766 1vqoD 177 1.04e+01 2fm8A 135 1.05e+01 2be3A 226 1.05e+01 1vq0A 302 1.05e+01 1gqeA 365 1.06e+01 e.38.1.1 70351 1wxiA 275 1.06e+01 1v76A 96 1.07e+01 1reoA 486 1.07e+01 c.3.1.2,d.16.1.5 97325,97326 1r26A 125 1.08e+01 c.47.1.1 96847 1vjjA 692 1.10e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1j7nA 776 1.12e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1bbpA 173 1.13e+01 1bbpA b.60.1.1 27147 1fjgD 209 1.13e+01 1c05A d.66.1.2 39553 1r62A 160 1.14e+01 d.122.1.3 104816 1g24A 211 1.14e+01 1g24A d.166.1.1 42270 2a1kA 233 1.15e+01 1qs1A 462 1.15e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1mhnA 59 1.15e+01 b.34.9.1 84964 1xocA 520 1.15e+01 1uacL 107 1.15e+01 b.1.1.1 99133 1i8kB 124 1.15e+01 b.1.1.1 71131 2a8lA 420 1.16e+01 1qznA 173 1.16e+01 b.2.2.2 104669 1s72T 120 1.17e+01 b.34.5.1 105339 1przA 252 1.18e+01 d.265.1.3 95064 1ts9A 102 1.18e+01 1a0p 290 1.18e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1fx3A 169 1.18e+01 1fx3B d.33.1.1 38524 2d37A 176 1.19e+01 1yqzA 438 1.19e+01 2d28C 149 1.19e+01 1i8dA 213 1.19e+01 b.43.4.3,b.43.4.3 61953,61954 1kwgA 645 1.21e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2bydA 323 1.21e+01 1m3iA 471 1.21e+01 f.9.1.1 91178 1maz 221 1.21e+01 1maz f.1.4.1 43393 2b5hA 200 1.22e+01 1s6yA 450 1.22e+01 c.2.1.5,d.162.1.2 105314,105315 1jj2Q 154 1.22e+01 1ffkO d.55.1.1 63102 1c0pA 363 1.24e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1e2tA 284 1.26e+01 1e2tA d.3.1.5 37121 1z57A 339 1.26e+01 2i1b 153 1.27e+01 2i1b b.42.1.2 25538 2cmd 312 1.27e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 2fa8A 105 1.28e+01 2cspA 130 1.29e+01 1sbxA 106 1.30e+01 a.6.1.4 105414 1iq4A 179 1.30e+01 1iq4A d.77.1.1 62641 1y14B 171 1.30e+01 1p6pA 125 1.30e+01 b.60.1.2 87839 1qwiA 143 1.30e+01 d.227.1.1 96474 1div 149 1.31e+01 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