# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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.soe.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 1l0qA 391 7.48e-11 b.1.3.1,b.69.2.3 77644,77645 2c4xA 260 1.66e-08 1b4rA 80 8.64e-04 1b4rA b.1.3.1 22072 1wgoA 123 2.47e-03 b.1.3.1 114618 3l5hA 589 4.76e-02 2yrlA 102 5.83e-02 1itbB 315 2.48e-01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 3ejjX 289 6.01e-01 1pz5B 220 6.27e-01 b.1.1.1,b.1.1.2 95403,95404 3d48R 211 6.79e-01 b.1.2.1,b.1.2.1 157289,157290 1f6fB 210 7.01e-01 1axiB b.1.2.1,b.1.2.1 22033,22034 1ev2E 220 8.56e-01 1cvsC b.1.1.4,b.1.1.4 21738,21739 3f7qA 234 9.15e-01 3cjjA 219 9.35e-01 2ghsA 326 1.08e+00 b.68.6.1 135209 3f7pC 248 1.27e+00 1hnf 182 1.38e+00 1qa9A 1hnfA 182 1.38e+00 b.1.1.1,b.1.1.3 19741,21680 3f7rA 249 1.61e+00 1q55A 880 1.65e+00 i.20.1.1 95862 3hr5B 226 1.92e+00 1qg3A 195 2.05e+00 1qg3A b.1.2.1,b.1.2.1 21993,21994 3l1oH 227 2.26e+00 3c12A 138 2.27e+00 3jz7A 214 2.51e+00 3d9aH 210 2.56e+00 2v3fA 505 2.63e+00 b.71.1.2,c.1.8.3 152453,152454 2nt0A 497 2.77e+00 b.71.1.2,c.1.8.3 138561,138562 1hilB 220 2.89e+00 1igtB b.1.1.1,b.1.1.2 19787,20897 3i2cH 222 2.97e+00 1cs6A 382 3.14e+00 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 3kstA 306 3.19e+00 1cl8A 276 3.22e+00 1ckqA c.52.1.1 33230 2wklA 497 3.32e+00 2h9fA 396 3.46e+00 d.21.1.4,d.21.1.4 147248,147249 3kldA 384 3.59e+00 3bgaA 1010 3.65e+00 3hxjA 330 3.66e+00 2w20A 471 3.72e+00 2vxsH 225 3.77e+00 1iuzA 98 3.87e+00 b.6.1.1 22861 1v6iA 232 4.21e+00 b.29.1.1 100383 2kpnA 103 4.27e+00 1jguH 217 4.34e+00 b.1.1.1,b.1.1.2 66688,66689 1fsoA 139 4.43e+00 1rhoA b.1.18.8 60007 2j43A 219 4.53e+00 b.3.1.3,b.3.1.3 147864,147865 3cfbB 213 4.57e+00 2eifA 136 4.95e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1pmyA 123 5.03e+00 b.6.1.1 22888 2ajuH 219 5.05e+00 1v8hA 107 5.18e+00 b.1.18.19 119870 2k7qA 191 5.34e+00 2j1vA 151 5.38e+00 3h8nA 195 5.40e+00 2w9dH 215 5.41e+00 2v5sA 394 5.58e+00 2jllA 389 5.72e+00 1o75A 415 6.17e+00 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 2a6zA 222 6.26e+00 b.29.1.13 126319 2fgqX 332 6.51e+00 f.4.3.1 133439 1bqk 124 6.84e+00 1bqk 1bqkA 124 6.84e+00 b.6.1.1 22889 2rikA 284 6.87e+00 3bz4B 217 7.54e+00 3m4wA 295 7.61e+00 1ollA 188 7.77e+00 b.1.1.4,b.1.1.4 93313,93314 2pooA 355 7.77e+00 1qlgA b.68.3.1 27626 3ef4A 124 7.88e+00 2ux7A 122 7.91e+00 3k5sA 217 8.26e+00 1vqoB 338 8.28e+00 b.43.3.2 120363 3hhrB 203 8.52e+00 1axiB b.1.2.1,b.1.2.1 22005,22006 1kcvH 217 8.57e+00 b.1.1.1,b.1.1.2 72315,72316 1ospH 218 8.70e+00 1igtB b.1.1.1,b.1.1.2 20117,21147 2iouG 535 9.17e+00 3hi7A 731 9.39e+00 1io1A 398 9.70e+00 1io1A e.32.1.1 62611 1a6zA 275 1.01e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1rie 129 1.07e+01 1rie 1rieA 129 1.07e+01 b.33.1.1 24427 2v5mA 388 1.07e+01 2w1nA 238 1.10e+01 2ipuG 226 1.10e+01 1q9rB 222 1.12e+01 b.1.1.1,b.1.1.2 96307,96308 3ejvA 179 1.12e+01 d.17.4.28 158181 3e8uH 217 1.12e+01 3l5jA 288 1.13e+01 1e54A 332 1.14e+01 1e54A f.4.3.1 59258 3l5iA 290 1.17e+01 1ncwH 222 1.24e+01 b.1.1.1,b.1.1.2 85555,85556 1f00I 282 1.26e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1pazA 123 1.37e+01 b.6.1.1 22878 1r6vA 671 1.38e+01 c.41.1.1 111710 3grwA 241 1.41e+01 2iwgB 181 1.43e+01 b.29.1.22 145548 1kdj 102 1.47e+01 1plc 1kdjA 102 1.47e+01 b.6.1.1 22864 1tlk 154 1.57e+01 1tlk 1ofzA 312 1.59e+01 b.68.8.1 86978 1kmtA 141 1.61e+01 b.1.18.8 77442 1yo8A 634 1.61e+01 2a77H 222 1.63e+01 b.1.1.2 126328 3k5rA 218 1.67e+01 2cwsA 237 1.79e+01 1py0A 125 1.87e+01 b.6.1.1 111645 2q9oA 559 1.90e+01 b.6.1.3,b.6.1.3,b.6.1.3 150149,150150,150151 3e0gA 483 1.91e+01 1wit 93 1.93e+01 1wit 1zpuA 534 1.96e+01 1fhgA 154 2.05e+01 1tlk b.1.1.4 21706 1am2 199 2.06e+01 1am2 1am2A 199 2.06e+01 b.86.1.2 28381 1w0nA 131 2.11e+01 b.18.1.28 114069 1xgyH 219 2.17e+01 b.1.1.2 121985 1h6lA 353 2.20e+01 b.68.3.1 60687 2ds0A 130 2.27e+01 3b2mA 295 2.31e+01 3cviH 219 2.35e+01 b.1.1.2 157010 1onqA 283 2.36e+01 b.1.1.2,d.19.1.1 93365,93366 1cfb 205 2.38e+01 1cfb 1cfbA 205 2.38e+01 b.1.2.1,b.1.2.1 21991,21992 3a8yA 392 2.44e+01 1uctA 218 2.45e+01 b.1.1.4,b.1.1.4 88467,88468 2imlA 199 2.46e+01 b.45.1.4 147729 2v90A 96 2.49e+01 1ecsA 126 2.49e+01 1ecsA d.32.1.2 59407 3h8tA 191 2.51e+01 3hurA 395 2.52e+01 1u58A 253 2.53e+01 b.1.1.2,d.19.1.1 144387,144388 1qlpA 394 2.55e+01 1ovaA e.1.1.1 42628 3gleA 295 2.56e+01 2aq5A 402 2.57e+01 3dorA 583 2.57e+01 1bhgA 613 2.59e+01 1bhgA b.1.4.1,b.18.1.5,c.1.8.3 22161,23766,28889 1nkr 201 2.61e+01 1nkr 1nkrA 201 2.61e+01 b.1.1.4,b.1.1.4 21799,21800 2ih8A 559 2.64e+01 b.6.1.3,b.6.1.3,b.6.1.3 137407,137408,137409 2je8A 848 2.64e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 147998,147999,148000,148001,148002 2b5uA 551 2.64e+01 b.101.1.1,b.110.1.1,h.4.9.1 127906,127907,127908 2qr5A 582 2.68e+01 b.69.7.2,c.69.1.33 151278,151279 2p4bA 295 2.71e+01 2pvrA 334 2.76e+01 d.144.1.7 149893 1olmA 403 2.81e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 2vjxA 846 2.85e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153203,153204,153205,153206,153207 2egeA 75 2.88e+01 2brqA 97 2.96e+01 b.1.18.10 129008 1nkiA 135 2.96e+01 d.32.1.2 91941 3emwA 217 2.97e+01 2rdyA 803 3.00e+01 2k7pA 188 3.01e+01 2ayh 214 3.03e+01 1axkA 2ayhA 214 3.03e+01 b.29.1.2 24172 3bqcA 335 3.04e+01 d.144.1.7 155497 2vr4A 846 3.08e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153495,153496,153497,153498,153499 1fw3A 275 3.08e+01 1qd5A f.4.2.1 60054 2vn4A 599 3.10e+01 3f2zA 159 3.10e+01 2petA 231 3.10e+01 1jj2B 337 3.11e+01 1ffkB b.43.3.2 63086 3bp6B 202 3.12e+01 3b5hA 184 3.14e+01 b.1.1.4,b.1.1.4 154838,154839 2iepA 192 3.20e+01 3mb7A 331 3.26e+01 1gzwA 134 3.27e+01 b.29.1.3 90535 2v9lA 274 3.28e+01 1axiB 236 3.31e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 2eigA 234 3.31e+01 3kykH 227 3.31e+01 1nqnA 122 3.33e+01 b.61.1.1 86042 2qo4A 126 3.33e+01 1wmdA 434 3.34e+01 b.18.1.20,c.41.1.1 109408,109409 2oz4A 265 3.34e+01 b.1.1.3,b.1.1.4,b.1.1.4 149099,149100,149101 1xgsA 295 3.34e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 3gldA 295 3.34e+01 3i2nA 357 3.36e+01 1itwA 741 3.36e+01 c.77.1.2 76793 2cy5A 140 3.37e+01 b.55.1.2 131018 3gb3A 235 3.37e+01 1y55X 126 3.40e+01 2q7nA 488 3.46e+01 3g0bA 740 3.48e+01 3iswA 99 3.48e+01 3mmyA 368 3.50e+01 3cmgA 667 3.52e+01 2fuqA 747 3.54e+01 2bnmA 198 3.59e+01 a.35.1.3,b.82.1.10 128835,128836 1i5pA 633 3.65e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2v43A 303 3.65e+01 1ymiA 334 3.65e+01 3lniA 213 3.69e+01 3gnmH 223 3.72e+01 3ggwB 217 3.73e+01 2w60A 218 3.77e+01 2idqA 105 3.84e+01 2ovrB 445 3.88e+01 a.158.1.1,b.69.4.1 145735,145736 1sfdA 105 3.88e+01 b.6.1.1 105480 1qf6A 642 3.89e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1fjgK 129 3.90e+01 1fjfK c.55.4.1 33733 2a38A 194 3.90e+01 2bvyA 475 3.92e+01 b.1.18.2,c.1.8.3 129301,129302 3ii1A 535 3.92e+01 1nfkA 325 3.94e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 2pltA 98 3.99e+01 b.6.1.1 22862 2w0pA 94 4.02e+01 b.1.18.10 153738 1yifA 533 4.04e+01 b.29.1.23,b.67.2.1 123283,123284 8fabB 224 4.06e+01 1igtB b.1.1.1,b.1.1.2 19773,20883 1qd6C 240 4.07e+01 1qd5A 1j83A 180 4.07e+01 b.18.1.12 66430 1uz8B 212 4.10e+01 b.1.1.1,b.1.1.2 108168,108169 2wd6A 349 4.16e+01 1b9mA 265 4.17e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 3djaA 579 4.18e+01 2hazA 105 4.27e+01 b.1.2.1 136303 3f9xA 166 4.28e+01 3dmmA 275 4.35e+01 2gc7A 386 4.37e+01 b.69.2.1 134954 2ov0A 105 4.38e+01 b.6.1.1 149033 1guiA 155 4.38e+01 b.18.1.14 76351 2bbkH 355 4.44e+01 2bbkH b.69.2.1 27634 2d5lA 706 4.45e+01 1vypX 364 4.45e+01 c.1.4.1 108905 1w1hA 151 4.53e+01 b.55.1.1 114076 2aabH 243 4.56e+01 b.1.1.2 126470 2abbA 364 4.57e+01 c.1.4.1 126517 1qd5A 275 4.60e+01 1qd5A f.4.2.1 43748 2wnwA 447 4.60e+01 3dkhA 559 4.61e+01 1um5H 217 4.66e+01 b.1.1.1,b.1.1.2 113302,113303 2hdwA 367 4.67e+01 1vyrA 364 4.67e+01 c.1.4.1 108906 3kolA 156 4.70e+01 2gbaA 105 4.70e+01 3hacA 728 4.71e+01 3acpA 417 4.74e+01 2blfA 373 4.75e+01 3lnfA 213 4.85e+01 1i4uA 181 4.89e+01 b.60.1.1 61732 2vkiA 148 4.89e+01 1eaxA 241 4.90e+01 b.47.1.2 64889 3e6hA 275 4.90e+01 2v44A 189 4.94e+01 1p16A 395 4.96e+01 b.40.4.6,d.142.2.3 87661,87662 3lnhA 213 5.01e+01 2hwzH 227 5.02e+01 1q7fA 286 5.02e+01 b.68.9.1 96036 3lneA 213 5.04e+01 3fgbA 361 5.09e+01 3a5xA 494 5.10e+01 2woyA 356 5.14e+01 2ao3A 130 5.16e+01 2zqoA 130 5.16e+01 b.42.2.1 154765 1j58A 385 5.22e+01 b.82.1.2 71531 3bp5B 202 5.23e+01 3licA 274 5.23e+01 1ynlH 219 5.24e+01 2r15A 212 5.26e+01 2cayA 145 5.27e+01 b.55.1.12 130167 1pqzA 238 5.30e+01 b.1.1.2,d.19.1.1 104297,104298 1r5mA 425 5.32e+01 2gtlO 215 5.36e+01 b.61.7.1,g.12.1.1,h.1.32.1 135673,135674,135675 2h3kA 144 5.37e+01 b.1.28.1 147218 1o59A 355 5.42e+01 b.18.1.22,b.18.1.22 92495,92496 1fjrA 195 5.42e+01 1fjrA b.102.1.1 59855 1yrzA 528 5.46e+01 b.29.1.23,b.67.2.1 123948,123949 4pazA 123 5.46e+01 b.6.1.1 22881 2bz6H 254 5.48e+01 b.47.1.2 129552 2dbjA 124 5.49e+01 3do7B 293 5.51e+01 2zaiA 497 5.58e+01 2h26A 291 5.58e+01 b.1.1.2,d.19.1.1 135990,135991 2hu5A 582 5.60e+01 b.69.7.2,c.69.1.33 136763,136764 2dd7A 216 5.60e+01 2e56A 144 5.62e+01 2z3zA 706 5.71e+01 2hft 218 5.73e+01 1boy 2hftA 218 5.73e+01 b.1.2.1,b.1.2.1 21951,21952 2dwcA 433 5.73e+01 2wwkO 109 5.79e+01 3fw6A 534 5.81e+01 1ravA 127 5.83e+01 1swuA b.61.1.1 27409 1w6nA 134 5.85e+01 b.29.1.3 114275 1a22B 238 5.94e+01 1axiB b.1.2.1,b.1.2.1 22003,22004 2hczX 245 5.98e+01 2x2uA 246 6.05e+01 2vqeK 129 6.06e+01 c.55.4.1 153435 1genA 218 6.07e+01 b.66.1.1 27536 2vxtH 216 6.11e+01 2j3mA 572 6.14e+01 1cczA 171 6.20e+01 1cczA b.1.1.1,b.1.1.3 19758,21683 2hahA 116 6.22e+01 3e7jA 749 6.22e+01 2gm6A 208 6.24e+01 b.82.1.19 147130 1l4dB 122 6.40e+01 d.15.5.1 77684 1cpnA 208 6.47e+01 b.29.1.2 24175 1pamA 686 6.47e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 3e6fA 274 6.47e+01 1ej6A 1289 6.52e+01 i.7.1.1 45967 1aac 105 6.53e+01 1aac 3libA 290 6.58e+01 1x84A 189 6.65e+01 d.113.1.2 121795 3g5bA 405 6.79e+01 2hrgA 496 6.86e+01 1n7vA 555 6.92e+01 b.126.1.1 85377 2uubK 129 6.96e+01 c.55.4.1 139942 1wbiA 129 6.99e+01 3a46A 289 7.03e+01 3lngA 215 7.23e+01 1ojrA 274 7.24e+01 c.74.1.1 93147 1nw3A 416 7.34e+01 c.66.1.31 86288 1arb 268 7.35e+01 1arb 1arbA 268 7.35e+01 b.47.1.1 25766 2ac3A 316 7.50e+01 1sqsA 242 7.50e+01 c.23.5.5 98968 2yugA 155 7.51e+01 1dqqB 210 7.53e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 2ii1A 301 7.61e+01 2p0dA 129 7.61e+01 1zkkA 167 7.68e+01 1vyfA 135 7.80e+01 b.60.1.2 108902 2pw0A 397 7.83e+01 1vioA 243 7.83e+01 d.265.1.3,d.66.1.5 100762,100763 1ukgA 252 7.84e+01 b.29.1.1 99489 1k32A 1045 7.86e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2volA 207 7.89e+01 2wp3T 102 7.90e+01 1f8eA 388 7.91e+01 2qwc b.68.1.1 59694 1qh5A 260 7.92e+01 1qh5A d.157.1.2 42057 1qqqA 264 7.92e+01 1bkpA d.117.1.1 40931