# List of top-scoring protein chains for t06-100-30-str2-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 2gp4A 628 1.74e-02 1v7lA 163 1.92e-02 1vs0A 310 8.65e-02 2napA 723 2.03e-01 2napA b.52.2.2,c.81.1.1 26926,35334 1zvyA 136 3.66e-01 1kqfA 1015 3.83e-01 b.52.2.2,c.81.1.1 72871,72872 1ofdA 1520 5.25e-01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1kblA 873 6.88e-01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1vkyA 347 7.61e-01 e.53.1.1 108696 1jsdA 319 9.71e-01 b.19.1.2 63258 1h0hA 977 1.14e+00 b.52.2.2,c.81.1.1 76435,76436 1r6xA 395 1.19e+00 b.122.1.3,c.26.1.5 97167,97168 1te7A 103 1.24e+00 2b3gA 123 1.28e+00 1rqpA 299 1.53e+00 b.141.1.1,c.132.1.1 97754,97755 1r3eA 309 1.54e+00 b.122.1.1,d.265.1.2 96907,96908 1o54A 277 1.78e+00 c.66.1.13 92482 1pueE 89 1.96e+00 1awcA a.4.5.21 16165 1ydxA 406 2.00e+00 2be1A 339 2.17e+00 2cz1B 212 2.51e+00 1vchA 175 2.87e+00 1xovA 326 3.13e+00 1k7jA 206 3.62e+00 d.115.1.1 72103 2ggcA 263 3.68e+00 1xnzA 264 3.70e+00 1w70A 60 3.85e+00 1wi1A 126 3.90e+00 1se8A 301 4.20e+00 b.40.4.3 105448 1q7hA 153 4.56e+00 b.122.1.1,d.17.6.2 96042,96043 1lgpA 116 4.62e+00 b.26.1.2 73890 2g50A 530 4.93e+00 1zymA 258 5.16e+00 1zymA a.60.10.1,c.8.1.2 18110,30705 1yfuA 174 5.16e+00 1jb0D 138 5.28e+00 1jb0D d.187.1.1 62823 1kl9A 182 5.44e+00 b.40.4.5 72681 1lucB 324 5.56e+00 1lucA c.1.16.1 29548 1zeqX 84 5.60e+00 1x6oA 174 5.63e+00 b.34.5.2,b.40.4.5 109493,109494 1upsA 420 5.79e+00 1bkb 136 6.36e+00 1bkb b.34.5.2,b.40.4.5 24609,25341 2fp8A 322 6.41e+00 1ugpB 226 6.56e+00 b.34.4.4 107832 1tvxA 75 6.56e+00 1tvxA d.9.1.1 37441 1ua4A 455 6.65e+00 c.72.1.3 99128 1t3tA 1303 6.65e+00 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 2fcbA 173 6.67e+00 2fcbA b.1.1.4,b.1.1.4 21781,21782 1dl5A 317 6.76e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1zx8A 136 6.94e+00 3ullA 132 6.96e+00 3ullA b.40.4.3 25282 2et1A 201 7.00e+00 1ktbA 405 7.17e+00 b.71.1.1,c.1.8.1 72960,72961 1jsmA 325 7.39e+00 b.19.1.2 63264 1kzlA 208 7.39e+00 b.43.4.3,b.43.4.3 77635,77636 1fi2A 201 7.46e+00 1fi2A b.82.1.2 59845 1p7tA 731 7.71e+00 c.1.13.1 94319 1qhxA 178 8.06e+00 1qhsA c.37.1.3 31936 1qvcA 145 8.27e+00 3ullA b.40.4.3 25284 1k3sA 113 8.69e+00 d.198.1.1 68120 2bj0A 203 8.71e+00 1iz6A 138 8.93e+00 b.34.5.2,b.40.4.5 76976,76977 1wmmA 145 9.00e+00 1zlmA 58 9.09e+00 1fltX 95 9.30e+00 1fltX b.1.1.4 21765 2bwvA 440 9.50e+00 1odmA 331 9.75e+00 b.82.2.1 86875 2g5dA 422 1.04e+01 1hr0W 71 1.07e+01 1ah9 b.40.4.5 25329 1xocA 520 1.08e+01 1k4iA 233 1.09e+01 d.115.1.2 72056 1pzxA 289 1.09e+01 c.119.1.1 95484 1zoiA 276 1.10e+01 1pk6A 133 1.12e+01 b.22.1.1 94801 2gjgA 248 1.13e+01 2g7jA 124 1.15e+01 1uheA 97 1.16e+01 1x7dA 350 1.17e+01 1qbjA 81 1.17e+01 1qbjA a.4.5.19 16155 1xmkA 79 1.23e+01 2b8mA 117 1.25e+01 1nkqA 259 1.26e+01 d.177.1.1 103862 1dzfA 215 1.28e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1yn8A 59 1.29e+01 1wyuB 474 1.29e+01 1r5mA 425 1.30e+01 1xneA 113 1.30e+01 2cnqA 306 1.31e+01 1obdA 306 1.36e+01 d.143.1.1 86767 1xm8A 254 1.37e+01 1sbyA 254 1.37e+01 2fbwA 621 1.38e+01 2h88A 621 1.38e+01 1fdr 248 1.42e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1j58A 385 1.43e+01 b.82.1.2 71531 1tf5A 844 1.44e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1twfF 155 1.46e+01 1xgsA 295 1.48e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1tksA 204 1.50e+01 d.115.1.2 107114 1y1nA 291 1.51e+01 1y0nA 78 1.52e+01 1uv4A 293 1.54e+01 2hcuA 213 1.56e+01 1aquA 297 1.57e+01 1aquA c.37.1.5 31942 1twfB 1224 1.63e+01 2h14A 317 1.65e+01 1ivyA 452 1.69e+01 1ivyA c.69.1.5 34654 1e0tA 470 1.70e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2frnA 278 1.72e+01 2gnqA 336 1.73e+01 1am2 199 1.74e+01 1am2 b.86.1.2 28381 2gu2A 312 1.75e+01 1snnA 227 1.76e+01 d.115.1.2 105821 1whzA 70 1.77e+01 2gs5A 198 1.78e+01 1kb0A 677 1.78e+01 a.3.1.6,b.70.1.1 68378,68379 1vdmA 153 1.79e+01 1amx 180 1.81e+01 1amx b.2.3.1 22410 1rcqA 357 1.81e+01 b.49.2.2,c.1.6.1 104882,104883 1zjcA 418 1.82e+01 2ha8A 184 1.89e+01 1zud2 66 1.90e+01 1ruwA 69 1.91e+01 1b12A 248 1.94e+01 1b12A b.87.1.2 28388 1wocA 103 1.94e+01 1v9kA 228 1.95e+01 d.265.1.3 108449 2cwpA 112 1.96e+01 1lam 484 1.96e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1zvhA 134 2.03e+01 2f9hA 129 2.08e+01 2fhfA 1083 2.11e+01 3tgl 269 2.15e+01 3tgl c.69.1.17 34733 1owfA 99 2.16e+01 a.55.1.1 87487 1pvxA 194 2.17e+01 1axkA b.29.1.11 24341 1aua 296 2.21e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1kcqA 104 2.23e+01 d.109.1.1 68449 1ju3A 583 2.26e+01 b.18.1.13,c.69.1.21 67300,67301 2fh1A 344 2.29e+01 1i12A 160 2.35e+01 1i21A d.108.1.1 61515 1vi6A 208 2.37e+01 c.23.15.1 100736 1pl8A 356 2.41e+01 b.35.1.2,c.2.1.1 94878,94879 2bjqA 345 2.43e+01 1o6aA 96 2.44e+01 b.139.1.1 92562 1n9lA 109 2.46e+01 d.110.3.6 85468 1rhfA 182 2.49e+01 b.1.1.1,b.1.1.4 97469,97470 1ykjA 394 2.51e+01 1cruA 454 2.51e+01 1c9uA b.68.2.1 27617 1a62 130 2.57e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1uebA 184 2.58e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1k0iA 394 2.59e+01 c.3.1.2,d.16.1.2 67942,67943 1e0bA 68 2.60e+01 1e0bA b.34.13.2 37476 2f2eA 146 2.61e+01 2as0A 396 2.64e+01 1v8bA 479 2.68e+01 1e5rA 290 2.73e+01 1e5rA b.82.2.4 59276 2f4pA 147 2.75e+01 1ti6A 875 2.81e+01 b.52.2.2,c.81.1.1 106974,106975 1nqzA 194 2.83e+01 d.113.1.1 86077 1jo8A 58 2.83e+01 b.34.2.1 71774 1o0xA 262 2.84e+01 d.127.1.1 80755 1ustA 93 2.88e+01 a.4.5.13 99884 1yn3A 98 2.88e+01 2a19A 175 2.91e+01 2fb6A 117 2.92e+01 1olzA 663 2.93e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1nnlA 225 2.94e+01 c.108.1.4 85906 1ifrA 121 2.97e+01 b.1.16.1 71203 1vm9A 111 2.97e+01 b.33.1.1 108886 2bjfA 329 3.00e+01 1lj5A 379 3.01e+01 e.1.1.1 73928 1yb2A 275 3.04e+01 2g1lA 104 3.07e+01 1sglA 209 3.08e+01 d.124.1.1 105536 1f0lA 535 3.09e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1i8dA 213 3.09e+01 b.43.4.3,b.43.4.3 61953,61954 1gcqA 61 3.13e+01 1ckaA b.34.2.1 60434 1h8eH 146 3.16e+01 1e79H b.93.1.1 60757 1fjgE 162 3.17e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1h2wA 710 3.18e+01 b.69.7.1,c.69.1.4 76596,76597 1v37A 177 3.21e+01 1gpr 162 3.24e+01 1gpr b.84.3.1 28267 2crvA 120 3.25e+01 2cxvA 219 3.28e+01 1k07A 263 3.32e+01 d.157.1.1 77218 1k82A 268 3.32e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1qj4A 257 3.33e+01 1qj4A c.69.1.20 34796 1vi4A 174 3.38e+01 c.8.7.1 100731 7aatA 401 3.39e+01 1ajsA c.67.1.1 34250 1q15A 503 3.43e+01 c.26.2.1,d.153.1.1 95538,95539 2h4uA 145 3.45e+01 1kicA 339 3.46e+01 c.70.1.1 72510 1lm8V 160 3.48e+01 b.3.3.1 74035 2gfaA 119 3.51e+01 1nnxA 109 3.52e+01 b.40.10.1 92013 1cl8A 276 3.53e+01 1ckqA c.52.1.1 33230 2b5hA 200 3.56e+01 1pwbA 177 3.72e+01 d.169.1.1,h.1.1.1 95212,95213 1zxq 192 3.74e+01 1zxq b.1.1.3,b.1.1.4 21657,21693 1fqtA 112 3.74e+01 1fqtA b.33.1.1 24441 1sq5A 308 3.74e+01 c.37.1.6 105882 1smxA 96 3.78e+01 b.40.4.5 105772 1svy 114 3.78e+01 1svy d.109.1.1 40831 1vr8A 142 3.85e+01 1wlsA 328 3.89e+01 2bikB 313 3.91e+01 1mzgA 146 4.03e+01 d.224.1.1 79696 1x3eA 165 4.04e+01 1jmuB 666 4.09e+01 1ylnA 252 4.11e+01 1zl0A 311 4.11e+01 1xtpA 254 4.12e+01 1jnyA 435 4.12e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1vraA 208 4.13e+01 1k0wA 231 4.14e+01 c.74.1.1 77220 1rxyA 253 4.14e+01 c.56.2.1 98065 2b5iD 217 4.18e+01 1ufmA 84 4.23e+01 a.4.5.47 107816 2f1rA 171 4.29e+01 1erjA 393 4.36e+01 1erjA b.69.4.1 27660 1xsqA 168 4.36e+01 1qxyA 252 4.38e+01 d.127.1.1 96565 1f2tB 148 4.39e+01 1f2tB 1wgvA 124 4.41e+01 1r17A 343 4.43e+01 b.2.3.4,b.2.3.4 96796,96797 2asbA 251 4.43e+01 4ubpB 126 4.47e+01 1ubpB b.85.3.1 28345 2cu3A 64 4.48e+01 1yfqA 342 4.48e+01 1khiA 176 4.51e+01 b.34.5.2,b.40.4.5 77408,77409 2aieP 203 4.57e+01 1mvfA 135 4.58e+01 b.1.1.1 85141 2f2hA 773 4.61e+01 1hl9A 449 4.61e+01 b.71.1.3,c.1.8.11 90650,90651 1cpt 412 4.65e+01 1cpt a.104.1.1 18968 1d5yA 292 4.67e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1hywA 68 4.70e+01 1hywA d.186.1.1 61425 1yb5A 351 4.72e+01 1yvhA 329 4.79e+01 1hn0A 1021 4.81e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 2bv4A 113 4.83e+01 1ztuA 341 4.85e+01 1vjkA 98 4.86e+01 d.15.3.1 108631 1lfkA 398 4.92e+01 a.104.1.1 77926 2gcc 70 4.92e+01 2gcc d.10.1.2 37484 1eaiC 61 4.93e+01 1eaiC g.22.1.1 44894 1owfB 94 4.94e+01 a.55.1.1 87488 1u7bA 261 4.95e+01 1ds1A 324 4.97e+01 1drtA b.82.2.2 28127 2an1A 292 5.03e+01 1zn6A 227 5.07e+01 1lk5A 229 5.07e+01 c.124.1.4,d.58.40.1 73960,73961 1w9sA 142 5.13e+01 2gf6A 135 5.16e+01 2cw5A 255 5.18e+01 1t1gA 364 5.19e+01 c.41.1.2 106246 1bteA 97 5.19e+01 1bteA g.7.1.3 44463 2b3hA 329 5.24e+01 2cdpA 160 5.25e+01 1fx2A 235 5.29e+01 1fx2A d.58.29.1 39430 1w96A 554 5.32e+01 1yb3A 175 5.33e+01 1hufA 140 5.33e+01 1hufA d.195.1.1 61272 1ro0A 216 5.33e+01 d.264.1.2 97664 1li4A 432 5.36e+01 c.2.1.4,c.23.12.3 84616,84617 2bdrA 175 5.54e+01 1m2tA 254 5.58e+01 d.165.1.1 84761 1e8pA 46 5.62e+01 g.55.1.1 59385 1zh1A 163 5.64e+01 1zm8A 259 5.66e+01 2b9sB 62 5.66e+01 1mk4A 157 5.74e+01 d.108.1.1 84979 1noa 113 5.78e+01 2mcm b.1.7.1 22208 1x74A 360 5.78e+01 2bmwA 304 5.78e+01 1qg3A 195 5.80e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1yliA 153 5.87e+01 1w66A 232 5.88e+01 1ckaA 57 5.88e+01 1ckaA b.34.2.1 24459 1jw9B 249 5.91e+01 c.111.1.1 67377 2apoA 357 5.92e+01 2fvgA 340 5.94e+01 2f23A 156 5.95e+01 1pch 88 6.06e+01 1ptf d.94.1.1 40564 1zhxA 438 6.09e+01 1s98A 107 6.14e+01 b.124.1.1 105377 1txqA 93 6.17e+01 1cqxA 403 6.17e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1f02T 66 6.19e+01 1f02T j.67.1.1 46360 1vkkA 154 6.24e+01 d.109.1.2 108669 1wn5A 130 6.25e+01 1n8jA 186 6.25e+01 c.47.1.10 85401 1lcyA 325 6.26e+01 b.36.1.4,b.47.1.1 73834,73835 2fhzB 108 6.28e+01 3il8 72 6.29e+01 1tvxA d.9.1.1 37356 1op3H 225 6.29e+01 b.1.1.1,b.1.1.2 87208,87209 1u8zA 168 6.33e+01 1rie 129 6.37e+01 1rie b.33.1.1 24427 2f15A 96 6.43e+01 1sv6A 269 6.48e+01 d.177.1.1 106043 1th0A 226 6.53e+01 d.3.1.7 106903 1oacA 727 6.62e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1g2bA 62 6.66e+01 1tud b.34.2.1 24488 2ch8A 201 6.66e+01 4dpvZ 584 6.69e+01 2cas b.121.5.2 23377 2fbyA 205 6.73e+01 1uunA 184 6.75e+01 f.6.1.2 100012 1zpsA 138 6.76e+01 1wi6A 88 6.76e+01 1f9zA 135 6.78e+01 1qipA d.32.1.1 38484 1izoA 417 6.79e+01 a.104.1.1 83851 1ctqA 166 6.80e+01 1ctqA c.37.1.8 31965 1gcqC 70 6.82e+01 1gcpA b.34.2.1 60436 3htsB 102 6.82e+01 2hts a.4.5.22 16175 2ew0A 192 6.94e+01 1rlmA 271 6.95e+01 1y8oB 128 6.96e+01 2ahrA 259 6.99e+01 1ghpA 258 7.00e+01 1btl e.3.1.1 60520 2d0oA 610 7.04e+01 1jztA 246 7.05e+01 c.104.1.1 63319 1riiA 265 7.07e+01 2eifA 136 7.12e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2bdvA 231 7.12e+01 1dg6A 191 7.13e+01 1d4vB b.22.1.1 23883 1fs0E 138 7.13e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1t9bA 677 7.17e+01 1kopA 223 7.18e+01 2cba b.74.1.1 27966 2bjuA 453 7.24e+01 1kolA 398 7.25e+01 b.35.1.2,c.2.1.1 77474,77475 1nu5A 370 7.34e+01 c.1.11.2,d.54.1.1 92183,92184 1bxoA 323 7.37e+01 2er7E b.50.1.2 26805 3cms 323 7.40e+01 1smrA b.50.1.2 26865 1orc 71 7.41e+01 1orc a.35.1.2 17054 1weyA 104 7.42e+01 2ff4A 388 7.44e+01 1iv8A 720 7.45e+01 b.71.1.1,c.1.8.1 76842,76843 1mqkH 127 7.47e+01 b.1.1.1 85053 2evwX 166 7.49e+01 2bokA 241 7.49e+01 1ayoA 130 7.54e+01 1ayoA b.2.4.1 22431 1by2 119 7.56e+01 1by2 d.170.1.1 42452 1ppjE 196 7.59e+01 b.33.1.1,f.23.12.1 104260,104261 1lbvA 252 7.59e+01 e.7.1.1 73813 1wkyA 464 7.60e+01 1rqwA 207 7.60e+01 b.25.1.1 97781 1n9eA 787 7.64e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1gttA 429 7.72e+01 d.177.1.1,d.177.1.1 70529,70530 1vpjA 192 7.79e+01 1yp5A 58 7.80e+01 1yzyA 413 7.85e+01 1suuA 312 7.86e+01 b.68.10.1 99006 1g5aA 628 7.86e+01 b.71.1.1,c.1.8.1 65152,65153 1rfs 139 7.87e+01 1rfs b.33.1.1 24434 1gk9B 557 7.90e+01 1q6hA 224 7.97e+01 d.26.1.1 95975 1obfO 335 7.98e+01 c.2.1.3,d.81.1.1 86768,86769 1z85A 234 8.01e+01 2as9A 210 8.04e+01 2cb5A 453 8.05e+01 3gcb d.3.1.1 37035 1mjuH 227 8.06e+01 b.1.1.1,b.1.1.2 91302,91303 1id2A 106 8.06e+01 1aac b.6.1.1 62288 1oruA 195 8.07e+01 b.58.1.2 93464 1xe1A 116 8.10e+01 b.43.3.1 109571 1pmhX 185 8.10e+01 b.18.1.18 104193 1ogiA 303 8.14e+01 b.43.4.2,c.25.1.1 92914,92915 1vc3B 97 8.19e+01 1tig 94 8.25e+01 1tig d.68.1.1 39566 1uedA 406 8.26e+01 a.104.1.1 99256 2covD 104 8.32e+01 1w6sA 599 8.33e+01 1qhfA 240 8.35e+01 1qhfA c.60.1.1 33960 1uj0A 62 8.45e+01 b.34.2.1 99449 1i1nA 226 8.45e+01 c.66.1.7 71102 1wdjA 187 8.47e+01 1zvkA 358 8.50e+01 1q5fA 156 8.54e+01 d.24.1.1 104536 1qwrA 319 8.58e+01 b.82.1.3 96491 1wxcB 134 8.63e+01 1o26A 232 8.65e+01 d.207.1.1 86566 1yavA 159 8.68e+01 2d1eA 248 8.73e+01 1kqfB 294 8.75e+01 d.58.1.5,f.23.22.1 75900,75901 1xfcA 384 8.75e+01 1z90A 469 8.77e+01 1fjrA 195 8.80e+01 1fjrA b.102.1.1 59855 1h8uA 117 8.80e+01 1h8uA d.169.1.1 60793 1tk9A 188 8.85e+01 c.80.1.3 107082 1uh4A 637 8.90e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1ji1A 637 8.94e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1mtpA 323 8.96e+01 e.1.1.1 85107 1s0aA 429 9.00e+01 c.67.1.4 98263 2aq5A 402 9.00e+01