# 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.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 1zhaA 267 4.31e-01 1pe1A 267 6.92e-01 c.1.10.4 94591 2pa6A 427 7.69e-01 1lroA 267 8.41e-01 c.1.10.4 78161 2nwrA 267 8.56e-01 2akzA 439 8.80e-01 c.1.11.1,d.54.1.1 126944,126945 2f6hX 419 9.53e-01 2r3bA 310 1.09e+00 3e0iA 267 1.47e+00 1o60A 292 1.62e+00 c.1.10.4 92532 2weyA 343 1.73e+00 2ixnA 310 2.07e+00 a.268.1.1 137777 3crvA 551 2.24e+00 2zumA 458 2.25e+00 2nvaA 372 2.50e+00 1iyxA 432 2.54e+00 c.1.11.1,d.54.1.1 83815,83816 2qikA 285 2.56e+00 2ivyA 101 2.58e+00 d.58.58.1 147817 3i16A 427 2.96e+00 1j5yA 187 3.39e+00 a.4.5.1,d.94.2.1 71592,71593 3e9aA 286 3.66e+00 1fmtA 314 3.72e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 3lerA 301 3.86e+00 3eweB 564 3.86e+00 2a11A 242 3.92e+00 2b0jA 358 3.99e+00 a.100.1.11,c.2.1.6 127639,127640 1rh9A 373 4.04e+00 c.1.8.3 118773 2ovyA 362 4.35e+00 2hyvA 308 4.41e+00 3bc9A 599 4.66e+00 2elcA 329 4.67e+00 a.46.2.1,c.27.1.1 146897,146898 2nnnA 140 4.69e+00 2vd3A 289 4.70e+00 2ousA 331 4.86e+00 3brjA 175 5.07e+00 a.285.1.1 155511 2pefA 373 5.41e+00 2pyyA 228 5.63e+00 1zcoA 262 5.97e+00 2i2wA 212 5.99e+00 1rj9A 304 6.23e+00 a.24.13.1,c.37.1.10 97553,97554 1kyqA 274 6.80e+00 c.2.1.11,e.37.1.1 73281,73282 3inpA 246 6.88e+00 2vh4A 381 6.91e+00 2nutB 753 6.94e+00 1ghsA 306 7.17e+00 1aq0A c.1.8.3 28840 1nofA 383 7.18e+00 b.71.1.2,c.1.8.3 92020,92021 2gzaA 361 7.36e+00 2i00A 406 7.50e+00 d.106.1.4,d.108.1.10 147466,147467 2o7iA 592 7.57e+00 2b9eA 303 7.62e+00 c.66.1.38 128124 1w6tA 444 7.86e+00 c.1.11.1,d.54.1.1 120670,120671 1rrmA 386 8.07e+00 e.22.1.2 105081 1dq3A 454 8.95e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1frpA 335 8.97e+00 1frpA e.7.1.1 42875 2qddA 378 9.19e+00 1vdeA 454 9.57e+00 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1nuyA 337 9.86e+00 e.7.1.1 86213 1zejA 293 1.01e+01 2ihyA 279 1.03e+01 2pa2A 151 1.03e+01 d.41.4.1 149337 1ml4A 308 1.04e+01 c.78.1.1,c.78.1.1 79255,79256 1ekeA 230 1.05e+01 1ekeA c.55.3.1 33572 3fvdA 378 1.06e+01 2fiwA 172 1.07e+01 d.108.1.1 133539 2d4xA 248 1.08e+01 2f8mA 244 1.12e+01 1or3A 165 1.12e+01 1nfn a.24.1.1 16522 3g65B 282 1.13e+01 1pcxA 810 1.16e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 2ganA 190 1.17e+01 d.108.1.1 134889 2hz5A 106 1.18e+01 d.110.7.1 147460 3ciwA 348 1.20e+01 3dagA 358 1.20e+01 2sqcA 631 1.21e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 3gg9A 352 1.21e+01 1dysA 348 1.22e+01 1bvwA c.6.1.1 30669 2cygA 312 1.24e+01 c.1.8.3 131025 2wzmA 283 1.25e+01 2nuwA 288 1.25e+01 1zymA 258 1.30e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1w53A 84 1.33e+01 a.186.1.2 109175 2aamA 309 1.35e+01 c.1.8.15 126489 1y1xA 191 1.37e+01 a.39.1.8 116374 2ot4A 525 1.40e+01 3f47A 358 1.40e+01 2nyvA 222 1.44e+01 1umpA 631 1.44e+01 a.102.4.2,a.102.4.2 99619,99620 1vr5A 547 1.44e+01 c.94.1.1 120437 2bzbA 62 1.47e+01 a.30.7.1 129556 1w7bA 339 1.47e+01 a.65.1.1 114317 1kkhA 317 1.50e+01 d.14.1.5,d.58.26.3 72645,72646 2a4vA 159 1.50e+01 c.47.1.10 126163 3brcA 156 1.51e+01 1wp1A 474 1.51e+01 f.5.1.1 114778 2btuA 346 1.53e+01 2b4gA 317 1.54e+01 c.1.4.1 127829 1u2zA 433 1.54e+01 c.66.1.31 107626 3a1jC 263 1.54e+01 1w3iA 293 1.55e+01 c.1.10.1 109152 2ekcA 262 1.57e+01 1np8A 159 1.58e+01 a.39.1.8 92022 1rjdA 334 1.59e+01 c.66.1.37 97558 1g6oA 330 1.59e+01 1g6oA c.37.1.11 32430 3hvyA 427 1.59e+01 1id1A 153 1.59e+01 1id1A c.2.1.9 62286 2d1hA 109 1.64e+01 a.4.5.50 131125 1ixmA 192 1.65e+01 1ixmA d.123.1.1 41114 2z43A 324 1.66e+01 1efyA 350 1.68e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 2aorA 223 1.68e+01 2glfA 450 1.69e+01 2a2fX 325 1.73e+01 3ifvA 247 1.75e+01 3fo3A 525 1.75e+01 3cuqA 234 1.76e+01 2j1pA 293 1.78e+01 1y4oA 104 1.79e+01 d.110.7.1 145901 3a5vA 397 1.81e+01 2z15A 130 1.84e+01 d.370.1.1 153921 1lk5A 229 1.87e+01 c.124.1.4,d.58.40.1 73960,73961 1pwhA 327 1.89e+01 c.79.1.1 95224 1hm6A 346 1.89e+01 1avc a.65.1.1 18147 2qi9C 249 1.92e+01 1r85A 379 1.92e+01 c.1.8.3 104839 1p0kA 349 1.92e+01 c.1.4.1 87648 1zz1A 369 1.93e+01 3kl4A 433 1.94e+01 1u14A 172 1.95e+01 c.51.4.3 107579 2i62A 265 1.97e+01 2pt7A 330 1.99e+01 c.37.1.11 149834 1vr6A 350 2.04e+01 c.1.10.4 120439 2felA 359 2.06e+01 3iruA 277 2.07e+01 1khtA 192 2.09e+01 c.37.1.1 84401 2ebfX 746 2.11e+01 a.296.1.1,c.150.1.2,d.3.1.17 146766,146767,146768 3d5kA 474 2.18e+01 2g19A 244 2.20e+01 2kl6A 114 2.23e+01 1b68A 191 2.24e+01 1nfn a.24.1.1 59076 3i99A 357 2.28e+01 2hzmA 212 2.30e+01 2i0xA 85 2.31e+01 d.58.58.1 147482 2c6qA 351 2.34e+01 1dfaA 454 2.35e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 3iixA 348 2.37e+01 2goyA 275 2.40e+01 1y8qA 346 2.41e+01 1ni3A 392 2.41e+01 c.37.1.8,d.15.10.2 80531,80532 1othA 321 2.42e+01 1othA c.78.1.1,c.78.1.1 35260,35261 3e3mA 355 2.43e+01 3cc8A 230 2.49e+01 1hrkA 359 2.53e+01 1hrkA c.92.1.1 61228 3ckjA 329 2.53e+01 1ixkA 315 2.53e+01 c.66.1.38 90716 2zvfA 171 2.55e+01 2npnA 251 2.55e+01 1vq0A 302 2.56e+01 d.193.1.1,g.81.1.1 114000,114001 3ip4A 485 2.58e+01 1vr0A 247 2.59e+01 c.148.1.1 120428 2bb6A 414 2.60e+01 1phkA 298 2.60e+01 d.144.1.7 41635 1j6oA 268 2.60e+01 c.1.9.12 77088 1wgzA 510 2.61e+01 1nxhA 126 2.63e+01 a.200.1.1 92300 1s3jA 155 2.67e+01 a.4.5.28 98437 3hoaA 509 2.74e+01 2fymA 431 2.74e+01 c.1.11.1,d.54.1.1 134379,134380 3bb7A 321 2.76e+01 1vquA 374 2.85e+01 2ehhA 294 2.85e+01 2i7aA 174 2.85e+01 1v9mA 323 2.86e+01 f.40.1.1 100543 3iduA 127 2.87e+01 2zy4A 546 2.89e+01 3gjwA 350 3.04e+01 2ivsA 314 3.07e+01 3daoA 283 3.08e+01 2hbtA 247 3.09e+01 1mxrA 375 3.10e+01 a.25.1.2 85197 1hw6A 278 3.17e+01 1frb c.1.7.1 61296 1dowA 205 3.17e+01 1dovA a.24.9.1 16626 1q06A 135 3.22e+01 a.6.1.3 95493 2nv1A 305 3.22e+01 1g5aA 628 3.23e+01 b.71.1.1,c.1.8.1 65152,65153 2j6gA 266 3.26e+01 3igoA 486 3.29e+01 2qltA 275 3.29e+01 2h5nA 133 3.32e+01 a.287.1.2 147227 3glrA 285 3.32e+01 2r91A 286 3.35e+01 1pjhA 280 3.39e+01 c.14.1.3 94761 1jbkA 195 3.41e+01 c.37.1.20 71631 1kwgA 645 3.42e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2zhjA 322 3.44e+01 2frnA 278 3.45e+01 c.66.1.47 133993 1gs9A 165 3.45e+01 a.24.1.1 83313 1wxqA 397 3.46e+01 c.37.1.8,d.15.10.2 121406,121407 1o5kA 306 3.48e+01 c.1.10.1 92504 1wouA 123 3.55e+01 c.47.1.16 109471 1g8xA 1010 3.56e+01 1lvk k.1.1.1 46378 1go3F 107 3.56e+01 a.60.8.2 65407 1zu4A 320 3.58e+01 1no5A 114 3.60e+01 d.218.1.5 92014 1c3cA 429 3.63e+01 1c3cA a.127.1.1 19425 1m0uA 249 3.64e+01 a.45.1.1,c.47.1.5 78359,78360 1htwA 158 3.64e+01 c.37.1.18 71083 1xikA 375 3.68e+01 1xikA a.25.1.2 16784 1mldA 314 3.79e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1phnB 172 3.83e+01 1qgwC a.1.1.3 15642 3hixA 106 3.87e+01 1k5dB 201 3.92e+01 b.55.1.3 68169 2douA 376 3.94e+01 1i76A 163 3.96e+01 1hfc d.92.1.11 61877 1np7A 489 3.97e+01 a.99.1.1,c.28.1.1 80677,80678 1ud0A 113 3.97e+01 a.8.4.1 99198 3fayA 387 3.98e+01 3fddA 533 3.99e+01 1mxsA 225 4.03e+01 c.1.10.1 91494 3c8tA 451 4.05e+01 3hnpA 353 4.05e+01 2rcyA 262 4.06e+01 1o4uA 285 4.07e+01 c.1.17.1,d.41.2.1 86624,86625 1m33A 258 4.09e+01 c.69.1.26 78514 1ufvA 276 4.10e+01 c.26.1.4 88487 1s0pA 176 4.11e+01 a.192.1.1 98300 1o17A 345 4.12e+01 a.46.2.1,c.27.1.1 80765,80766 1z91A 147 4.16e+01 a.4.5.28 124736 3e5jA 403 4.21e+01 3kczA 368 4.24e+01 1v8dA 235 4.26e+01 c.140.1.1 108425 3abaA 403 4.26e+01 1v8fA 276 4.32e+01 c.26.1.4 100503 2qe6A 274 4.33e+01 1wy2A 351 4.33e+01 1vmaA 306 4.34e+01 a.24.13.1,c.37.1.10 108887,108888 2hcfA 234 4.37e+01 c.108.1.6 136333 1c96A 753 4.42e+01 1amj c.8.2.1,c.83.1.1 30727,35403 2r8wA 332 4.43e+01 1kcvH 217 4.43e+01 b.1.1.1,b.1.1.2 72315,72316 1dcoA 104 4.43e+01 1dcpA d.74.1.1 39680 1uzeA 589 4.43e+01 d.92.1.5 108174 1ybtA 184 4.51e+01 1qsdA 106 4.51e+01 1qsdA a.7.5.1 16335 1itwA 741 4.52e+01 c.77.1.2 76793 3ld9A 223 4.52e+01 3e9vA 120 4.54e+01 d.370.1.1 158072 3eglA 277 4.56e+01 3k6rA 278 4.58e+01 2j6lA 500 4.60e+01 1j9aA 184 4.61e+01 c.55.3.5 84135 1o58A 303 4.61e+01 c.79.1.1 92491 3c9uA 342 4.63e+01 d.79.4.1,d.139.1.1 156144,156145 1jm6A 407 4.64e+01 a.29.5.1,d.122.1.4 66876,66877 3lxmA 335 4.64e+01 2ps2A 371 4.67e+01 3gykA 175 4.67e+01 2rccA 346 4.74e+01 2fp4B 395 4.74e+01 c.23.4.1,d.142.1.4 133897,133898 1q2lA 939 4.75e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 3fjvA 194 4.83e+01 1p1xA 260 4.85e+01 c.1.10.1 104060 3f44A 220 4.85e+01 2pocA 367 4.89e+01 1m2kA 249 4.91e+01 c.31.1.5 84754 1ug7A 128 4.94e+01 a.24.24.1 107824 3g3tA 295 4.97e+01 3ilmA 141 4.98e+01 2ftrA 108 4.99e+01 d.58.4.15 134077 1pv9A 348 5.02e+01 c.55.2.1,d.127.1.1 95157,95158 3ca8A 266 5.07e+01 3bjaA 139 5.12e+01 2nv2A 294 5.14e+01 2orwA 184 5.16e+01 2ifuA 307 5.22e+01 2wadA 680 5.25e+01 2gpyA 233 5.26e+01 3h9pA 249 5.33e+01 1csh 435 5.36e+01 1csh 1cshA 435 5.36e+01 a.103.1.1 18880 2bleA 367 5.36e+01 2gokA 429 5.38e+01 b.92.1.10,c.1.9.17 147145,147146 2z20A 432 5.39e+01 2cyyA 151 5.42e+01 a.4.5.32,d.58.4.2 131028,131029 1e4yA 214 5.42e+01 1zin c.37.1.1,g.41.2.1 31901,45181 3ei9A 432 5.43e+01 2puzA 419 5.44e+01 b.92.1.10,c.1.9.17 149873,149874 3dadA 339 5.46e+01 3griA 424 5.47e+01 2zy5A 546 5.49e+01 1xg5A 279 5.52e+01 c.2.1.2 115277 1otvA 259 5.63e+01 a.132.1.4 93526 1rxdA 159 5.63e+01 c.45.1.1 111959 2fmyA 220 5.77e+01 1rqbA 539 5.78e+01 a.5.7.2,c.1.10.5 105057,105058 1mdbA 539 5.84e+01 e.23.1.1 79008 2evrA 246 5.89e+01 b.34.11.3,d.3.1.16 132440,132441 3fnbA 405 5.96e+01 2zdrA 349 5.96e+01 b.85.1.1,c.1.10.6 154398,154399 1z9hA 290 5.97e+01 a.45.1.1,c.47.1.5 124758,124759 1mhsA 920 5.98e+01 i.18.1.1 79130 2rdcA 153 5.98e+01 2qdxA 257 5.99e+01 2qv3A 457 5.99e+01 2qwwA 154 6.01e+01 2ccjA 205 6.02e+01 1vd5A 377 6.03e+01 a.102.1.7 108518 1jalA 363 6.04e+01 c.37.1.8,d.15.10.2 84138,84139 2dyoA 297 6.05e+01 1g4yB 101 6.06e+01 1g4yB f.15.1.1 60251 1dofA 403 6.11e+01 1c3cA a.127.1.1 19429 1snyA 267 6.14e+01 c.2.1.2 105833 2zbtA 297 6.21e+01 1avpA 204 6.25e+01 1avpA d.3.1.7 37132 2g38B 198 6.25e+01 a.25.4.2 134550 3exaA 322 6.26e+01 3fbgA 346 6.27e+01 2nvoA 535 6.27e+01 1xahA 354 6.28e+01 2v8qA 157 6.33e+01 d.129.6.2 152781 1x13A 401 6.36e+01 1qnxA 209 6.40e+01 1qnxA d.111.1.1 40914 2yzrA 330 6.42e+01 1by0A 27 6.42e+01 h.4.6.1 45795 1f4qA 165 6.47e+01 1alvA a.39.1.8 17360 1yyvA 131 6.48e+01 a.4.5.69 124254 1nlnA 204 6.53e+01 d.3.1.7 91962 1eudB 396 6.55e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 2z3yA 662 6.55e+01 a.4.1.18,c.3.1.2,d.16.1.5 154024,154025,154026 3gmiA 357 6.60e+01 3hhpA 312 6.60e+01 1ytaA 180 6.61e+01 c.55.3.5 124002 2zhgA 154 6.64e+01 3ilkA 244 6.68e+01 1v47A 349 6.68e+01 b.122.1.3,c.26.1.5 100292,100293 2kavA 129 6.71e+01 2rgxA 206 6.74e+01 1bjt 793 6.77e+01 1bjt 1bjtA 793 6.77e+01 e.11.1.1 43249 1pg5A 299 6.78e+01 c.78.1.1,c.78.1.1 104146,104147 1vqvA 306 6.84e+01 d.79.4.1,d.139.1.1 114024,114025 1cfzA 162 6.86e+01 1cfzA c.56.1.1 33754 1qwkA 317 6.89e+01 c.1.7.1 96482 2h09A 155 6.89e+01 3bqkA 360 6.90e+01 3i0zA 389 6.90e+01 2dkoA 146 6.92e+01 2d58A 107 6.95e+01 1vdmA 153 6.97e+01 c.61.1.1 119994 1twfF 155 6.97e+01 a.143.1.2 112731 1y10A 407 6.99e+01 2yvyA 278 6.99e+01 1yf9A 171 6.99e+01 d.20.1.1 123054 1gweA 503 7.09e+01 e.5.1.1 70667 1m1nB 522 7.13e+01 c.92.2.3 78418 2hnkA 239 7.16e+01 1gakA 141 7.18e+01 1gakA a.19.1.1 16415 1zckA 154 7.18e+01 2gw8A 114 7.19e+01 3h0gF 142 7.20e+01 2ptrA 462 7.20e+01 1jbeA 128 7.20e+01 3chy c.23.1.1 62845 3exrA 221 7.23e+01 2d5rB 116 7.24e+01 d.370.1.1 146467 1bg4A 302 7.27e+01 c.1.8.3 28806 1df0A 700 7.27e+01 1dkvA a.39.1.8,b.14.1.1,d.3.1.3 17375,23674,37106 2nrjA 346 7.28e+01 h.4.4.2 148378 1zx4A 192 7.33e+01 2cmd 312 7.35e+01 2cmd 2cmdA 312 7.35e+01 c.2.1.5,d.162.1.1 30135,42102 2egxA 269 7.35e+01 1p9qC 256 7.45e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2di4A 238 7.46e+01 a.269.1.1 131522 1k94A 165 7.48e+01 a.39.1.8 68333 1j8yF 297 7.51e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1al3 324 7.52e+01 1al3 1al3A 324 7.52e+01 c.94.1.1 35835 1yliA 153 7.52e+01 d.38.1.1 123651 3dlcA 219 7.54e+01 2p10A 286 7.65e+01 c.1.12.9 149144 1l7mA 211 7.66e+01 c.108.1.4 73664 1or4A 178 7.67e+01 a.1.1.2 93447 1hbzA 498 7.68e+01 1cf9A e.5.1.1 60937 2ip2A 334 7.69e+01 2eg2A 112 7.73e+01 3k89A 314 7.74e+01 2z00A 426 7.78e+01 2bpqA 373 7.81e+01 1mp9A 198 7.82e+01 d.129.1.1,d.129.1.1 91385,91386 1r5jA 337 7.82e+01 c.77.1.5 97097 1p91A 269 7.83e+01 c.66.1.33 94378 2eisA 133 7.85e+01 3ezsA 376 7.86e+01 1x4tA 92 7.88e+01 a.2.15.1 121698 3io1A 445 7.93e+01 1sc6A 404 7.96e+01 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 2hszA 243 7.97e+01 c.108.1.6 136726