# List of top-scoring protein chains for t2k-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.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 2ox7A 155 5.18e-01 b.172.1.1 149054 1ispA 181 5.76e-01 c.69.1.18 76778 2h1tA 188 6.69e-01 b.178.1.1 147215 1i6wA 181 7.49e-01 1i6wA c.69.1.18 61859 3d2fA 675 8.13e-01 5gcnA 166 1.05e+00 1yghA d.108.1.1 40807 1z9lA 128 1.19e+00 3gwaA 365 1.35e+00 3e8tA 220 1.38e+00 2dexX 671 1.77e+00 b.2.9.1,b.6.1.6,d.126.1.5 131436,131437,131438 1wdaA 670 1.82e+00 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 2q4vA 170 2.03e+00 d.108.1.1 139878 3gkuA 225 2.29e+00 3d3yA 425 2.50e+00 3enbA 222 3.29e+00 c.55.3.14 158189 1g60A 260 3.40e+00 c.66.1.11 70151 3f9sA 146 3.95e+00 1bolA 222 3.96e+00 1bolA d.124.1.1 41120 1rsy 152 4.20e+00 1rsy 1rsyA 152 4.20e+00 b.7.1.2 23192 1yghA 164 4.27e+00 1yghA d.108.1.1 40802 1jmmA 377 4.35e+00 b.30.6.1 71749 1qstA 160 4.39e+00 1yghA d.108.1.1 40804 2z6cA 129 4.56e+00 3bn0A 112 4.88e+00 d.27.1.1 155425 2wjrA 214 5.38e+00 1jnuA 104 5.52e+00 d.110.3.6 71762 3bbjA 272 5.74e+00 3h5lA 419 6.32e+00 3ioxA 497 6.45e+00 3l8bA 906 6.67e+00 2v0uA 146 6.75e+00 1yt5A 258 6.76e+00 1clqA 903 6.79e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 3ipkA 497 6.97e+00 1q7fA 286 7.10e+00 b.68.9.1 96036 2qxlA 658 7.30e+00 2ea7A 434 7.38e+00 3lzjA 903 7.51e+00 1bynA 128 7.54e+00 1rsy b.7.1.2 23193 3g9hA 328 7.79e+00 1aisB 200 8.43e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 3e4wA 320 8.49e+00 1u1sA 82 8.59e+00 b.38.1.2 119451 1bw0A 416 9.12e+00 1bw0A c.67.1.1 34385 3f04A 143 9.34e+00 2r7hA 177 9.50e+00 1ih7A 903 9.54e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 2nxpA 156 9.84e+00 d.379.1.1 148504 2axqA 467 1.00e+01 2obdA 476 1.01e+01 3go2A 409 1.05e+01 2wkqA 332 1.05e+01 2wkrA 332 1.05e+01 3dy0A 336 1.13e+01 2h26A 291 1.13e+01 b.1.1.2,d.19.1.1 135990,135991 2oo6A 409 1.14e+01 1mylA 53 1.15e+01 1bazA a.43.1.1 17427 3gqhA 163 1.21e+01 1qmyA 167 1.23e+01 1qmyA d.3.1.2 37094 1gzcA 239 1.24e+01 b.29.1.1 70803 1hk9A 74 1.30e+01 b.38.1.2 83541 1n9lA 109 1.30e+01 d.110.3.6 85468 1ig9A 903 1.31e+01 1clqA c.55.3.5,e.8.1.1 62367,62368 1ew4A 106 1.37e+01 1ew4A d.82.2.1 40023 1w0pA 781 1.38e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 3h1qA 272 1.41e+01 1kit 757 1.41e+01 1kit 2carA 196 1.43e+01 c.51.4.1 130161 1bdtA 53 1.45e+01 1bazA a.43.1.1 17433 2z2vA 365 1.46e+01 3gqnA 772 1.49e+01 2jzbB 74 1.49e+01 2esnA 310 1.56e+01 a.4.5.37,c.94.1.1 132333,132334 2wkpA 332 1.64e+01 1wtjA 343 1.65e+01 3lhnA 126 1.66e+01 1zgsA 447 1.69e+01 1gzqA 300 1.75e+01 b.1.1.2,d.19.1.1 70818,70819 1dkzA 219 1.75e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2w36A 225 1.80e+01 1v9cA 218 1.84e+01 c.23.17.1 100533 3f7xA 151 1.86e+01 2izpA 303 1.87e+01 a.250.1.1 137826 2wmiB 606 1.87e+01 1m1sA 116 1.87e+01 b.1.11.2 84747 1hx6A 394 1.88e+01 1cjdA b.121.2.1,b.121.2.1 58995,58996 2zu1A 183 1.95e+01 1cy5A 97 1.95e+01 1cy5A a.77.1.3 18430 1hn4A 131 1.96e+01 a.133.1.2 65893 1odtC 318 1.97e+01 c.69.1.25 86885 1x3zA 335 1.97e+01 d.3.1.4 121673 1cx8A 639 2.02e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1btn 106 2.05e+01 1btn 1btnA 106 2.05e+01 b.55.1.1 26952 2halA 212 2.05e+01 b.47.1.4 136289 3gwfA 540 2.07e+01 2w2sA 202 2.08e+01 1cbgA 490 2.14e+01 c.1.8.4 28933 1cwwA 102 2.14e+01 1cy5A a.77.1.3 18434 2vfkA 205 2.14e+01 1qmvA 197 2.25e+01 1qq2A c.47.1.10 33066 3isyA 120 2.31e+01 3mmcA 418 2.38e+01 1ut1A 148 2.40e+01 b.2.3.6 108014 2oaaA 249 2.41e+01 1xahA 354 2.42e+01 1dkxA 219 2.46e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1kaeA 434 2.48e+01 c.82.1.2 72247 1v5vA 401 2.52e+01 b.44.2.1,d.250.1.1 113539,113540 2qg3A 208 2.54e+01 3ihkA 218 2.58e+01 1v8hA 107 2.58e+01 b.1.18.19 119870 1qq2A 199 2.58e+01 1qq2A c.47.1.10 33064 1tljA 213 2.60e+01 d.282.1.1 107126 3lfmA 495 2.61e+01 2v3gA 283 2.63e+01 c.1.8.3 152457 1mspA 126 2.64e+01 1mspA b.1.11.2 22333 1t7vA 278 2.65e+01 b.1.1.2,d.19.1.1 112302,112303 2d9zA 129 2.70e+01 2citA 282 2.73e+01 c.1.8.3 130499 2uubP 88 2.75e+01 d.27.1.1 139947 3lzaA 141 2.79e+01 2ygsA 92 2.80e+01 1cy5A a.77.1.3 18431 3gbxA 420 2.80e+01 1iyeA 309 2.80e+01 e.17.1.1 83786 1tf1A 198 2.84e+01 d.110.2.2 106826 2bv9A 290 2.85e+01 c.1.8.3 129242 2btzA 394 2.89e+01 1l4dB 122 2.91e+01 d.15.5.1 77684 1led 243 2.94e+01 1led 1ledA 243 2.94e+01 b.29.1.1 24039 1jm6A 407 2.96e+01 a.29.5.1,d.122.1.4 66876,66877 1hqlA 257 2.99e+01 b.29.1.1 65907 1ge8A 249 2.99e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1xpjA 126 3.07e+01 c.108.1.18 115739 1uocA 289 3.09e+01 c.55.3.9 99686 2wmgA 581 3.12e+01 1nn7A 105 3.12e+01 d.42.1.2 85894 1rtwA 220 3.12e+01 a.132.1.3 97823 1z4rA 168 3.13e+01 d.108.1.1 124444 2wmfA 581 3.13e+01 2irfG 113 3.14e+01 2irfG a.4.5.23 16185 2wmhA 581 3.18e+01 3fouA 156 3.23e+01 1ydyA 356 3.24e+01 c.1.18.3 123006 1a7j 290 3.30e+01 1a7j 1a7jA 290 3.30e+01 c.37.1.6 31952 1b56A 135 3.31e+01 b.60.1.2 27183 3e7wA 511 3.38e+01 1otkA 249 3.40e+01 a.25.1.2 93521 1nykA 165 3.45e+01 b.33.1.1 86408 3c1qA 123 3.46e+01 3i3wA 443 3.49e+01 3hd0A 237 3.60e+01 3crkA 407 3.66e+01 2cxvA 219 3.68e+01 b.47.1.4 131012 3h8vA 292 3.68e+01 2hc5A 117 3.73e+01 d.352.1.1 147255 1z2iA 358 3.75e+01 3gzbA 154 3.75e+01 1z5hA 780 3.76e+01 1bmlC 362 3.81e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 2r2nA 425 3.83e+01 3duzA 487 3.84e+01 3d36A 244 3.87e+01 3gwiA 170 3.90e+01 1vf1A 229 3.91e+01 3biyA 380 3.96e+01 2jf7A 532 4.01e+01 1prxA 224 4.06e+01 1prxA c.47.1.10 33076 2cdcA 366 4.06e+01 3e8vA 82 4.07e+01 1g8aA 227 4.07e+01 c.66.1.3 90506 1bdyA 123 4.07e+01 1bdyA b.7.1.1 23190 3eebA 209 4.14e+01 3hurA 395 4.15e+01 2vqeP 88 4.19e+01 i.1.1.1 153440 2gtqA 867 4.22e+01 2w7qA 204 4.23e+01 1t8qA 336 4.24e+01 c.1.18.3 106669 1co6A 107 4.33e+01 1ycc a.3.1.1 15894 2gduA 504 4.40e+01 b.71.1.1,c.1.8.1 135032,135033 1kcgC 178 4.40e+01 d.19.1.1 68440 2mspA 126 4.41e+01 1mspA b.1.11.2 22335 1l7aA 318 4.42e+01 c.69.1.25 77772 3bjoA 103 4.43e+01 1fzoA 274 4.43e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1b7nA 130 4.43e+01 3lzt d.2.1.2 36468 3clqA 421 4.45e+01 3ibwA 88 4.50e+01 2fy7A 287 4.55e+01 1xccA 220 4.55e+01 c.47.1.10 115113 2ns9A 157 4.58e+01 d.129.3.10 148382 2yxmA 100 4.61e+01 1r64A 481 4.62e+01 b.18.1.20,c.41.1.1 97140,97141 1hl2A 297 4.63e+01 c.1.10.1 83581 2pq8A 278 4.64e+01 1fjgP 88 4.64e+01 1emwA d.27.1.1 38444 2id4A 503 4.66e+01 b.18.1.20,c.41.1.1 137265,137266 2vw9A 134 4.72e+01 1mzuA 129 4.73e+01 d.110.3.1 79714 1ywmA 200 4.74e+01 2j6vA 301 4.74e+01 1ot5A 477 4.77e+01 b.18.1.20,c.41.1.1 87409,87410 1p32A 209 4.79e+01 1p32A d.25.1.1 38379 1havA 217 4.81e+01 1havA b.47.1.4 26423 2rr3A 130 4.84e+01 1wakA 397 4.91e+01 1cliA 345 4.92e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2aq5A 402 4.92e+01 1pztA 286 4.92e+01 c.68.1.2 95470 2icwG 213 4.95e+01 a.202.1.1 137251 3abiA 365 5.09e+01 1u6rA 380 5.10e+01 a.83.1.1,d.128.1.2 119600,119601 1xe0A 114 5.12e+01 b.121.3.1 115197 2f99A 153 5.13e+01 d.17.4.9 147011 3b7nA 320 5.25e+01 2wmiA 606 5.27e+01 3cuqC 176 5.29e+01 3kkgA 146 5.34e+01 1mykA 53 5.36e+01 1bazA a.43.1.1 17425 1nal3 297 5.37e+01 1nal3 2fsrA 195 5.38e+01 d.108.1.1 134036 2hlvA 160 5.43e+01 2uubR 88 5.46e+01 a.4.8.1 139949 1r7aA 504 5.47e+01 b.71.1.1,c.1.8.1 97192,97193 2wbsA 89 5.48e+01 1ykjA 394 5.50e+01 c.3.1.2,d.16.1.2 145914,145915 2jh2A 148 5.53e+01 b.2.2.2 148053 1fgxA 288 5.54e+01 1fgxA c.68.1.2 34508 2cy2A 174 5.55e+01 d.108.1.1 131016 3cniA 156 5.59e+01 1dfoA 417 5.59e+01 1bj4A c.67.1.4 34480 1qn2A 100 5.63e+01 1ycc a.3.1.1 15882 2q07A 306 5.66e+01 b.122.1.1,c.18.1.4,d.17.6.5 149981,149982,149983 1yqyA 523 5.66e+01 d.92.1.14,d.166.1.1 123903,123904 1jpyA 137 5.70e+01 g.17.1.6 67065 2bwqA 129 5.71e+01 b.7.1.2 129380 1zupA 315 5.73e+01 c.55.3.11 125681 1g2rA 100 5.75e+01 1g2rA d.192.1.1 60231 1d8jA 81 5.76e+01 1d8jA a.4.5.18 16153 1rowA 109 5.83e+01 b.1.11.2 97676 2f31A 233 5.83e+01 1r5iD 216 5.84e+01 a.202.1.1 97091 3licA 274 5.86e+01 1fzkA 274 5.88e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 2jzfA 143 5.94e+01 1yroB 286 5.94e+01 c.68.1.2 123932 2c27A 315 5.95e+01 d.108.1.1 129659 1a6zA 275 5.96e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 2nqrA 411 5.98e+01 b.85.6.1,b.103.1.1,c.57.1.2 138490,138491,138492 1upvA 257 6.00e+01 a.123.1.1 113398 3go9A 492 6.00e+01 2zuyA 620 6.02e+01 1nmmB 286 6.09e+01 c.68.1.2 80662 1nf5B 286 6.09e+01 c.68.1.2 80454 1obpA 159 6.12e+01 1obpA b.60.1.1 27092 1g8lA 411 6.16e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1nal1 297 6.18e+01 1nal3 2gj3A 120 6.19e+01 1e5pA 151 6.25e+01 1bj7 b.60.1.1 59272 2jzdA 129 6.25e+01 2wmkA 606 6.30e+01 1mb4A 370 6.30e+01 c.2.1.3,d.81.1.1 78908,78909 2oxgA 108 6.30e+01 2z8gA 549 6.33e+01 3inoA 143 6.35e+01 1i9yA 347 6.38e+01 1i9yA d.151.1.2 62101 1qwtA 255 6.38e+01 b.26.1.3 96501 1i9zA 347 6.45e+01 1i9yA d.151.1.2 62102 2bo9B 222 6.46e+01 d.17.1.5,d.17.1.5 128898,128899 1a66A 178 6.52e+01 1a02N b.2.5.3 22441 2w3yA 283 6.52e+01 2bneA 241 6.61e+01 c.73.1.3 128824 3brcA 156 6.62e+01 3dw0A 294 6.62e+01 2wk7A 393 6.63e+01 2r6oA 294 6.64e+01 1uby 367 6.67e+01 1uby 3kxeC 88 6.71e+01 3fqiA 417 6.76e+01 1dmtA 696 6.76e+01 1dmtA d.92.1.4 40296 1x0cA 549 6.77e+01 1gt1A 159 6.78e+01 b.60.1.1 90515 1lk2A 274 6.86e+01 b.1.1.2,d.19.1.1 91056,91057 1wu3I 161 6.92e+01 a.26.1.3 114890 1r0uA 148 6.93e+01 b.60.1.5 96741 2v4iB 213 6.93e+01 1nbuC 119 6.94e+01 d.96.1.3 91769 1nbuA 119 6.95e+01 d.96.1.3 91767 1nbuB 119 6.97e+01 d.96.1.3 91768 1auk 489 6.97e+01 1auk 1aukA 489 6.97e+01 c.76.1.2 35030 2voaA 257 6.98e+01 1h8gA 95 6.98e+01 b.109.1.1 65735 1ignA 246 7.00e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 3kphA 217 7.15e+01 1hroA 106 7.18e+01 1ycc a.3.1.1 15897 2q6fA 309 7.21e+01 2wzpP 326 7.24e+01 1l4zB 136 7.26e+01 d.15.5.1 77704 3hwpA 302 7.27e+01 1w36C 1122 7.27e+01 c.37.1.19,c.37.1.19,c.52.1.25 114125,114126,114127 1sjwA 144 7.29e+01 d.17.4.9 98899 3iwlA 68 7.31e+01 2f4mA 295 7.32e+01 d.3.1.4 145135 1v4sA 455 7.32e+01 c.55.1.3,c.55.1.3 100309,100310 1grwA 126 7.32e+01 b.1.11.2 70391 1fe0A 68 7.32e+01 1cc8A d.58.17.1 39345 2bryA 497 7.35e+01 2a1iA 146 7.43e+01 c.52.1.20 125999 1js8A 394 7.45e+01 a.86.1.1,b.112.1.1 67219,67220 3lkeA 263 7.45e+01 1xmtA 103 7.47e+01 d.108.1.1 115561 3a63A 365 7.47e+01 1pq9A 253 7.51e+01 a.123.1.1 95004 1fdyA 297 7.52e+01 1nal3 c.1.10.1 29071 1mjnA 179 7.52e+01 c.62.1.1 79210 2jkgA 179 7.54e+01 2cxxA 190 7.56e+01 c.37.1.8 131013 2o0i1 180 7.57e+01 2cw8A 537 7.59e+01 2w2gA 264 7.60e+01 2ezvA 269 7.67e+01 1hv2A 99 7.68e+01 d.42.1.1 61287 2b33A 140 7.72e+01 d.79.1.1 127765 1r1hA 696 7.76e+01 d.92.1.4 104756 1npeA 267 7.79e+01 b.68.5.1 92032 1nycA 111 7.82e+01 b.61.2.2 92336 2brqA 97 7.86e+01 b.1.18.10 129008 2r6fA 972 7.95e+01 3hczA 148 7.96e+01 3hyjA 198 7.96e+01 2gwmA 200 7.96e+01