# List of top-scoring protein chains for t04-100-30-alpha-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 1htp 131 8.30e-04 1htp 1hpcA 131 1.60e-03 1htp b.84.1.1 28221 1zkoA 136 2.19e-03 1a65A 504 3.20e-03 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1nr0A 611 5.22e-03 b.69.4.1,b.69.4.1 86078,86079 2ov0A 105 7.57e-03 2gbaA 105 8.84e-03 1hfuA 503 9.06e-03 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1aac 105 1.06e-02 1aac 2idqA 105 1.11e-02 1gycA 499 1.36e-02 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1bxaA 105 1.45e-02 1aac b.6.1.1 22839 2evbA 74 1.54e-02 1sfdA 105 2.06e-02 b.6.1.1 105480 1bdo 80 2.26e-02 1bdo 1bdoA 80 2.26e-02 b.84.1.1 28214 1vrbA 342 2.31e-02 b.82.2.11 120450 1x82A 190 3.10e-02 b.82.1.7 114955 1brwA 433 3.22e-02 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1yu4A 381 3.30e-02 b.163.1.1,d.169.1.8 124033,124034 1qxrA 189 3.59e-02 b.82.1.7 96552 1sv6A 269 3.98e-02 d.177.1.1 106043 2e63A 170 4.20e-02 1ti6B 274 4.32e-02 b.3.5.1,d.58.1.5 106976,106977 1yu0A 381 5.15e-02 b.163.1.1,d.169.1.8 124025,124026 1id2A 106 6.02e-02 1aac b.6.1.1 62288 1us8A 147 6.08e-02 c.37.1.12 99859 2be1A 339 6.40e-02 1yu1A 381 6.45e-02 b.163.1.1,d.169.1.8 124027,124028 2gc1A 188 6.50e-02 b.82.1.7 134928 1hxn 219 6.67e-02 1hxn 1hxnA 219 6.67e-02 b.66.1.1 27529 1n26A 325 6.90e-02 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 2glwA 92 7.53e-02 2gcuA 245 8.25e-02 3tdt 274 8.45e-02 3tdt 3tdtA 274 8.45e-02 b.81.1.2 28053 1yu2A 381 8.69e-02 b.163.1.1,d.169.1.8 124029,124030 1k8mA 93 9.18e-02 b.84.1.1 68314 1seiA 130 9.41e-02 1seiA d.140.1.1 41463 2dsjA 423 9.45e-02 1yu3A 381 9.54e-02 b.163.1.1,d.169.1.8 124031,124032 1zi0A 307 1.05e-01 2gaiA 633 1.17e-01 1v10A 521 1.19e-01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1tdtA 259 1.31e-01 3tdt b.81.1.2 28055 1gx3A 284 1.37e-01 d.3.1.5 70678 2a6hC 1119 1.38e-01 e.29.1.1 126264 1y8oB 128 1.45e-01 b.84.1.1 122759 1gpr 162 1.50e-01 1gpr 1gprA 162 1.50e-01 b.84.3.1 28267 2i45A 107 1.52e-01 2vesA 299 1.58e-01 1cb8A 678 1.59e-01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1xrkA 124 1.60e-01 d.32.1.2 115881 1ghj 79 1.66e-01 1ghj 1fm4A 159 1.69e-01 1bv1 d.129.3.1 76186 2qt6A 498 1.80e-01 1w5rA 278 1.80e-01 d.3.1.5 120643 2hrgA 496 1.84e-01 2hc8A 113 1.86e-01 1f2tA 149 2.05e-01 1f2tA c.37.1.12 32373 3btxA 204 2.32e-01 1gttA 429 2.35e-01 d.177.1.1,d.177.1.1 70529,70530 1dgwA 178 2.38e-01 1dgwA b.82.1.2 28090 3b6hA 498 2.44e-01 1orvA 728 2.55e-01 b.70.3.1,c.69.1.24 87354,87355 2czrA 226 2.58e-01 1m1hA 248 2.63e-01 b.114.1.1,d.58.42.1 78415,78416 1vdzA 588 2.68e-01 1o4tA 133 2.78e-01 b.82.1.9 86622 1gwmA 153 2.80e-01 b.18.1.19 83348 1aozA 552 2.85e-01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 2g3mA 693 2.86e-01 1ru4A 400 2.99e-01 b.80.1.9 97836 1yfuA 174 3.09e-01 b.82.1.20 123094 1nkqA 259 3.25e-01 d.177.1.1 103862 1mrgA 263 3.28e-01 d.165.1.1 42183 2j2zB 173 3.32e-01 2dfuA 264 3.37e-01 2j82A 240 3.46e-01 2qnkA 286 3.86e-01 2e9qA 459 4.02e-01 1pmyA 123 4.19e-01 b.6.1.1 22888 1pguA 615 4.42e-01 b.69.4.1,b.69.4.1 88069,88070 2gllA 171 4.43e-01 2eenA 183 4.59e-01 2f41A 121 4.64e-01 d.38.1.5 132904 1k82A 268 4.67e-01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 2r15A 212 4.69e-01 2chhA 114 4.72e-01 b.115.1.1 130471 3c6kA 381 5.04e-01 2aujD 309 5.17e-01 1k32A 1045 5.35e-01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1vmeA 410 5.54e-01 c.23.5.1,d.157.1.3 108893,108894 2z4iA 233 5.58e-01 2i8dA 123 5.58e-01 1uqxA 113 5.60e-01 b.115.1.1 99801 1at0 145 5.68e-01 1at0 1at0A 145 5.68e-01 b.86.1.1 28374 2cxxA 190 5.77e-01 c.37.1.8 131013 2btiA 63 5.88e-01 2uvfA 608 5.95e-01 2dyiA 162 6.03e-01 3cnwA 148 6.18e-01 1z6bA 154 6.38e-01 d.38.1.6 124510 2ea7A 434 6.41e-01 2qfmA 364 6.47e-01 1k4zA 159 6.69e-01 b.80.5.1 72070 2b5iD 217 6.90e-01 g.18.1.1,g.18.1.1 127900,127901 1nbcA 155 7.02e-01 1nbcA b.2.2.2 22390 2onfA 140 7.30e-01 1uz5A 402 7.59e-01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1v25A 541 7.68e-01 e.23.1.1 108275 1ep0A 185 7.76e-01 1dzrA b.82.1.1 28080 1pbyA 489 7.88e-01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1pz7A 204 7.94e-01 b.29.1.4 95405 1j1lA 290 8.09e-01 b.82.1.12 90766 1o9gA 250 8.15e-01 c.66.1.29 86692 2fmyA 220 8.16e-01 2qxvA 361 8.37e-01 1bv1 159 8.39e-01 1bv1 1qi7A 253 8.73e-01 1qi7A d.165.1.1 42210 2e4qA 109 9.16e-01 2q1fA 1022 9.29e-01 2nxcA 254 9.34e-01 c.66.1.39 138739 2qv3A 457 9.47e-01 2b0vA 153 9.57e-01 d.113.1.1 127650 2p17A 277 9.69e-01 2sli 679 1.02e+00 2sli 2sliA 679 1.02e+00 b.29.1.9,b.68.1.1 24274,27611 1y9lA 115 1.04e+00 1uebA 184 1.07e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1hmt 132 1.08e+00 1hmt 1hmtA 132 1.08e+00 b.60.1.2 27169 2qggA 182 1.10e+00 1mzyA 333 1.13e+00 b.6.1.3,b.6.1.3 103848,103849 1tq5A 242 1.13e+00 b.82.1.12 119311 1lktA 104 1.14e+00 1lktA b.90.1.1 28398 1nwbA 124 1.18e+00 b.124.1.1 86296 1vr8A 142 1.22e+00 d.312.1.1 120445 1b56A 135 1.25e+00 b.60.1.2 27183 1kafA 108 1.27e+00 d.199.1.1 68372 2iagA 482 1.27e+00 2qm1A 326 1.30e+00 1vj2A 126 1.33e+00 b.82.1.10 100796 1v6iA 232 1.33e+00 b.29.1.1 100383 2a22A 215 1.38e+00 d.159.1.7 126025 3b98A 475 1.38e+00 1w9yA 319 1.38e+00 b.82.2.1 120801 2qdlA 165 1.43e+00 1uy4A 145 1.44e+00 b.18.1.10 108131 1t5hX 504 1.47e+00 e.23.1.1 106449 1rc6A 261 1.50e+00 b.82.1.11 97287 1yymG 313 1.52e+00 d.172.1.1 124232 1zeqX 84 1.55e+00 2hrvA 142 1.59e+00 2hrvA b.47.1.4 26429 1ef8A 261 1.66e+00 1ef8A c.14.1.3 30921 2cw8A 537 1.67e+00 1bpoA 494 1.68e+00 1bpoA a.118.1.4,b.69.6.1 19143,27670 1wp5A 323 1.68e+00 b.68.10.1 114780 2ys3A 137 1.69e+00 2bgcA 238 1.74e+00 a.4.5.4,b.82.3.3 128458,128459 3bjsA 428 1.74e+00 1yqfA 203 1.78e+00 d.25.1.1 123880 1k5cA 335 1.78e+00 b.80.1.3 72076 1pazA 123 1.78e+00 b.6.1.1 22878 1xgsA 295 1.81e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 1sbxA 106 1.81e+00 a.6.1.4 105414 1j1yA 136 1.83e+00 d.38.1.5 90776 2biwA 490 1.83e+00 1rjcA 137 1.84e+00 2z14A 133 1.87e+00 2in0A 139 1.92e+00 1yx0A 159 1.92e+00 d.108.1.1 124168 1i9gA 280 1.93e+00 c.66.1.13 62090 2obwA 258 1.93e+00 3brgC 427 1.95e+00 1vrmA 325 1.95e+00 d.96.2.1 120472 2pz4A 239 1.95e+00 1xs1A 193 1.96e+00 b.85.4.1 115892 1oj4A 283 1.97e+00 d.14.1.5,d.58.26.5 93083,93084 1lf7A 182 1.97e+00 b.60.1.1 73878 1ub0A 258 1.97e+00 c.72.1.2 88394 2h0vA 338 2.01e+00 2b06A 155 2.02e+00 d.113.1.1 127624 1jyhA 157 2.04e+00 d.60.1.3 71956 2qedA 258 2.06e+00 1l1nA 183 2.13e+00 b.47.1.4 73476 1ri6A 343 2.14e+00 b.69.11.1 97503 2q8kA 401 2.15e+00 2ftwA 521 2.23e+00 b.92.1.3,c.1.9.6 134083,134084 1wzoA 246 2.25e+00 1vyqA 173 2.25e+00 b.85.4.1 120548 1cx4A 305 2.27e+00 b.82.3.2,b.82.3.2 59099,59100 1fqtA 112 2.28e+00 1fqtA b.33.1.1 24441 1vpzA 73 2.32e+00 b.151.1.1 113998 1e2tA 284 2.33e+00 1e2tA d.3.1.5 37121 2p9oA 169 2.35e+00 1yhfA 115 2.36e+00 b.82.1.9 123176 1gyhA 318 2.36e+00 b.67.2.1 70757 2qk0A 74 2.37e+00 1whi 122 2.38e+00 1whi 1whiA 122 2.38e+00 b.39.1.1 24810 2vroA 532 2.39e+00 2v24A 208 2.39e+00 2inwA 133 2.44e+00 d.110.8.1 137533 1juvA 193 2.46e+00 c.71.1.1 90912 1i52A 236 2.48e+00 1i52A c.68.1.13 61767 2obfA 289 2.49e+00 1bteA 97 2.49e+00 1bteA g.7.1.3 44463 1xfpA 142 2.50e+00 b.1.1.1 109587 1xe1A 116 2.50e+00 b.43.3.1 109571 2e8gA 241 2.52e+00 1p32A 209 2.54e+00 1p32A d.25.1.1 38379 2aioA 269 2.55e+00 d.157.1.1 126829 2q6fA 309 2.58e+00 2phlA 397 2.59e+00 1dgwA b.82.1.2,b.82.1.2 28082,28083 1efvA 315 2.60e+00 1efvA c.26.2.3,c.31.1.2 31633,31728 3c8wA 255 2.63e+00 2j8gA 339 2.63e+00 1hp1A 516 2.65e+00 d.114.1.1,d.159.1.2 70976,70977 2p3eA 420 2.65e+00 2eifA 136 2.68e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1l8rA 101 2.70e+00 a.6.1.4 73700 1x1oA 286 2.70e+00 2qo4A 126 2.71e+00 1zkcA 197 2.78e+00 b.62.1.1 125182 1y0yA 353 2.78e+00 b.49.3.1,c.56.5.4 122514,122515 1sixA 174 2.80e+00 b.85.4.1 98892 2e27H 126 2.82e+00 2qe7H 135 2.83e+00 1u24A 337 2.84e+00 c.45.1.4 112968 2cw5A 255 2.85e+00 1zelA 298 2.85e+00 1ixlA 131 2.86e+00 d.38.1.5 90717 1wxcB 134 2.89e+00 1mq7A 154 2.93e+00 b.85.4.1 79404 1oe1A 336 2.95e+00 b.6.1.3,b.6.1.3 86891,86892 2ichA 335 2.96e+00 1zdsA 336 3.00e+00 b.6.1.3,b.6.1.3 124952,124953 1y3tA 337 3.01e+00 b.82.1.5 122600 2d5lA 706 3.03e+00 1v70A 105 3.12e+00 b.82.1.9 113555 1shyB 551 3.23e+00 b.69.12.1,g.16.2.1 105565,105566 2d4rA 147 3.26e+00 d.129.3.6 131256 1r75A 141 3.28e+00 b.134.1.1 97189 1ush 550 3.29e+00 1ush 2j6bA 109 3.32e+00 d.321.1.1 138078 2j4hA 193 3.37e+00 1uurA 473 3.40e+00 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1rdo1 113 3.41e+00 1rtm1 1xksA 450 3.42e+00 b.69.14.1 115422 1jxhA 288 3.46e+00 c.72.1.2 67415 1op3H 225 3.46e+00 b.1.1.1,b.1.1.2 87208,87209 1p0iA 529 3.49e+00 c.69.1.1 93867 2o62A 270 3.50e+00 2cohA 202 3.56e+00 a.4.5.4,b.82.3.2 130677,130678 1lmeA 176 3.57e+00 d.167.1.1 84629 2fl7A 232 3.62e+00 2gzqA 200 3.67e+00 2zcwA 202 3.71e+00 1o54A 277 3.74e+00 c.66.1.13 92482 2hsiA 282 3.74e+00 1ex0A 731 3.76e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1yb5A 351 3.77e+00 b.35.1.2,c.2.1.1 116601,116602 1u0tA 307 3.78e+00 e.52.1.1 107567 1smlA 269 3.78e+00 1smlA d.157.1.1 42053 2r3uA 211 3.86e+00 2z2nA 299 3.87e+00 2eigA 234 3.88e+00 2nvaA 372 3.89e+00 1wzcA 249 3.93e+00 c.108.1.10 121491 1zx6A 58 3.94e+00 2yu1A 451 3.95e+00 2dfbA 190 3.98e+00 b.29.1.11 131470 2p1gA 249 3.99e+00 2o6pA 161 4.06e+00 1ow1A 195 4.07e+00 b.131.1.3 93625 1f8eA 388 4.15e+00 2qwc b.68.1.1 59694 2pmlX 348 4.15e+00 3bh7B 352 4.16e+00 2awaA 390 4.17e+00 2hrdA 253 4.18e+00 1hdhA 536 4.22e+00 c.76.1.2 65805 1v4sA 455 4.28e+00 c.55.1.3,c.55.1.3 100309,100310 2qdxA 257 4.33e+00 1r5mA 425 4.34e+00 2qcpX 80 4.42e+00 2z3zA 706 4.44e+00 2isnA 364 4.47e+00 2bkyX 89 4.48e+00 d.68.6.1 128717 1omoA 322 4.51e+00 c.2.1.13 104017 1h1aA 191 4.56e+00 b.29.1.11 83450 2gu9A 113 4.62e+00 2cu2A 337 4.62e+00 1jj2P 95 4.67e+00 1ffkN b.34.5.1 63101 1gydB 315 4.70e+00 b.67.2.1 70751 1x3mA 415 4.73e+00 c.55.1.2,c.55.1.2 121664,121665 1xfoA 357 4.75e+00 b.49.3.1,c.56.5.4 115265,115266 2g72A 289 4.79e+00 c.66.1.15 134724 1lfoA 127 4.80e+00 b.60.1.2 27223 2jrnA 163 4.82e+00 1vpvA 300 4.84e+00 c.119.1.1 113975 1omiA 248 4.87e+00 b.82.3.3,a.4.5.4 87079,87080 2bbvA 363 4.88e+00 2bbvA b.121.4.4 23323 2v2gA 233 4.89e+00 2b4uA 335 4.90e+00 2e1zA 415 4.93e+00 1poiA 317 4.96e+00 1poiA c.124.1.2 34153 2g8sA 353 4.97e+00 2bnmA 198 4.97e+00 a.35.1.3,b.82.1.10 128835,128836 2rdyA 803 4.99e+00 1bxvA 91 5.03e+00 1aac b.6.1.1 22875 2fhqA 141 5.04e+00 b.45.1.1 133497 2q30A 110 5.07e+00 2i8aA 252 5.08e+00 1snrA 341 5.12e+00 b.6.1.3,b.6.1.3 105823,105824 1bb9 115 5.13e+00 1bb9 1bb9A 115 5.13e+00 b.34.2.1 24554 2et1A 201 5.14e+00 b.82.1.2 132351 2h26A 291 5.16e+00 b.1.1.2,d.19.1.1 135990,135991 1vqoQ 96 5.19e+00 b.34.5.1 120378 1yllA 200 5.21e+00 b.82.1.17 123653 1qniA 581 5.22e+00 1qniA b.6.1.4,b.69.3.1 23042,27642 1mdbA 539 5.24e+00 e.23.1.1 79008 1zo0A 126 5.24e+00 d.108.1.7 125416 2ftbA 125 5.26e+00 b.60.1.2 134057 1jdc 429 5.34e+00 1jdc 1jdcA 429 5.34e+00 b.71.1.1,c.1.8.1 27789,28776 1vllA 334 5.34e+00 c.2.1.13 108834 1fi2A 201 5.35e+00 1fi2A b.82.1.2 59845 1tmxA 293 5.38e+00 1im3D 95 5.41e+00 1im3D b.1.18.5 62568 2b4pA 334 5.50e+00 2gauA 232 5.51e+00 a.4.5.4,b.82.3.2 134894,134895 2gjgA 248 5.55e+00 2q6kA 283 5.58e+00 3begB 115 5.61e+00 2bazA 142 5.61e+00 2qf3A 243 5.64e+00 2f9hA 129 5.74e+00 b.161.1.1 133162 1j9qA 341 5.81e+00 1nif b.6.1.3,b.6.1.3 62765,62766 2g1lA 104 5.83e+00 b.26.1.2 134520 2hy1A 280 5.84e+00 1z47A 355 5.85e+00 1pexA 207 5.94e+00 b.66.1.1 27540 2h0bA 184 6.04e+00 1y6hA 177 6.05e+00 d.167.1.1 116505 2fw2A 260 6.08e+00 c.14.1.3 134231 1h8gA 95 6.12e+00 b.109.1.1 65735 2ppeA 343 6.13e+00 2jerA 389 6.14e+00 1eybA 471 6.14e+00 1ey2A b.82.1.4 28115 1k5dB 201 6.19e+00 b.55.1.3 68169 1dfcA 493 6.28e+00 1dfcA b.42.5.1,b.42.5.1,b.42.5.1,b.42.5.1 25616,25617,25618,25619 1sawA 225 6.32e+00 d.177.1.1 112050 2imqX 282 6.32e+00 2iwkA 642 6.34e+00 2b2nA 344 6.36e+00 c.37.1.19 127710 1l0qA 391 6.39e+00 b.1.3.1,b.69.2.3 77644,77645 2b5nA 323 6.40e+00 2gxfA 142 6.46e+00 2rn2 155 6.51e+00 2rn2 2aq5A 402 6.56e+00 1xnkA 196 6.58e+00 b.29.1.11 122195 2ux7A 122 6.58e+00 2r77A 205 6.62e+00 2b7uA 257 6.63e+00 1nrkA 328 6.64e+00 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