# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1gqzA 274 1.56e-08 d.21.1.1,d.21.1.1 83311,83312 2gkeA 274 2.72e-08 1bwzA 274 5.69e-08 1bwzA d.21.1.1,d.21.1.1 38337,38338 1w61A 414 3.07e-07 1tm0A 350 1.86e-06 d.21.1.3 107147 1qyaA 307 1.21e-04 d.21.1.2,d.21.1.2 104653,104654 1sdjA 310 1.22e-04 d.21.1.2,d.21.1.2 98807,98808 1ym5A 300 2.05e-04 2azpA 318 4.59e-04 1t6kA 278 5.24e-04 1u1wA 298 1.28e-03 1xubA 298 1.82e-03 1u0kA 288 2.92e-02 d.21.1.2,d.21.1.2 107547,107548 1s7jA 262 3.10e-02 d.21.1.2 98647 2g6yA 217 1.35e-01 1hzdA 272 4.29e-01 c.14.1.3 65969 2exrA 524 4.35e-01 1oe4A 247 6.92e-01 c.18.1.3 86895 1w9hA 427 7.57e-01 1r6lA 239 8.21e-01 d.14.1.4,d.101.1.1 97153,97154 1wc3A 219 1.04e+00 1t9hA 307 1.18e+00 1sr8A 298 1.49e+00 e.54.1.1 105959 2ghsA 326 1.61e+00 1u9yA 284 1.79e+00 1h8eD 482 1.99e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1kvkA 395 2.05e+00 d.14.1.5,d.58.26.3 73060,73061 2a35A 215 2.34e+00 1fecA 490 2.65e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1umzA 278 2.85e+00 b.29.1.2 99639 1lj5A 379 3.00e+00 e.1.1.1 73928 1ut9A 609 3.03e+00 a.102.1.2,b.1.18.2 99912,99913 1c8uA 285 3.19e+00 1c8uA d.38.1.3,d.38.1.3 38547,38548 1xtqA 177 3.26e+00 1ab8A 220 3.44e+00 1azsA d.58.29.1 39414 1wz8A 264 3.57e+00 1u6zA 513 4.24e+00 1ycoA 279 4.64e+00 1v61A 132 4.74e+00 b.55.1.1 108389 2ck3D 482 4.90e+00 1s31A 273 5.33e+00 1y43B 173 5.86e+00 1ass 159 6.71e+00 1a6dA c.8.5.2 30818 1cl8A 276 6.86e+00 1ckqA c.52.1.1 33230 1o54A 277 7.03e+00 c.66.1.13 92482 1c8zA 265 7.03e+00 1c8zA d.23.1.1 38375 1eb6A 177 7.13e+00 d.92.1.12 64895 1go7P 462 7.14e+00 b.80.7.1,d.92.1.6 76245,76246 1v7wA 807 7.43e+00 a.102.1.4,b.30.5.3 108411,108412 1tc5A 194 7.54e+00 c.110.1.1 106752 1k7iA 479 7.65e+00 b.80.7.1,d.92.1.6 77281,77282 1lcl 142 7.98e+00 1lcl b.29.1.3 24216 2fimA 276 8.73e+00 1ojjA 402 8.77e+00 b.29.1.10 93130 1gyvA 120 9.05e+00 b.1.10.2 70790 1t6cA 315 9.16e+00 c.55.1.8,c.55.1.8 106558,106559 1gz6A 319 9.50e+00 c.2.1.2 76410 1cv8 174 9.53e+00 1cv8 d.3.1.1 37089 2d0oA 610 9.58e+00 1mh1 186 1.00e+01 1eesA c.37.1.8 32002 1p4uA 153 1.01e+01 b.1.10.2 87780 2a7bA 120 1.01e+01 2a6zA 222 1.02e+01 1orvA 728 1.02e+01 b.70.3.1,c.69.1.24 87354,87355 1s2kA 206 1.03e+01 b.29.1.20 98389 1k32A 1045 1.03e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1eemA 241 1.08e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1q2lA 939 1.08e+01 1ur4A 399 1.12e+01 1iu1A 146 1.17e+01 b.1.10.2 71428 2a7kA 250 1.18e+01 1a9xB 379 1.18e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1n0wA 243 1.28e+01 c.37.1.11 79772 1bjt 793 1.28e+01 1bjt e.11.1.1 43249 1hdkA 141 1.38e+01 b.29.1.3 65807 2a84A 300 1.40e+01 1yg9A 330 1.40e+01 1xe0A 114 1.41e+01 1e79D 482 1.45e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1wmsA 177 1.46e+01 c.37.1.8 109414 1zbqA 327 1.48e+01 1ep3B 262 1.51e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1j5pA 253 1.53e+01 d.81.1.3,c.2.1.3 71577,83092 1d8cA 723 1.56e+01 1d8cA c.1.13.1 29325 1udxA 416 1.58e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1b65A 375 1.60e+01 1b65A d.154.1.1 42020 2a9fA 398 1.63e+01 1t5rA 284 1.64e+01 f.6.1.1 106465 1oygA 447 1.64e+01 b.67.2.2 93726 1h65A 270 1.66e+01 c.37.1.8 65640 2blnA 305 1.67e+01 1j48A 110 1.68e+01 b.1.7.1 84112 1ciy 590 1.71e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1ac5 483 1.73e+01 1ac5 c.69.1.5 34653 2bk7B 222 1.74e+01 2bo9B 222 1.74e+01 1nxzA 246 1.74e+01 b.122.1.2,c.116.1.5 86391,86392 2a1fA 247 1.78e+01 1erjA 393 1.81e+01 1erjA b.69.4.1 27660 1dhkB 223 1.97e+01 1led b.29.1.1 24157 1hl9A 449 2.04e+01 b.71.1.3,c.1.8.11 90650,90651 1nbwA 607 2.08e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1suwA 249 2.09e+01 e.52.1.1 106027 1gttA 429 2.13e+01 d.177.1.1,d.177.1.1 70529,70530 1c30B 382 2.13e+01 c.8.3.1,c.23.16.1 30736,31413 2akaB 299 2.15e+01 1fobA 334 2.19e+01 c.1.8.3 83255 1dymA 402 2.22e+01 1celA b.29.1.10 24304 1kkhA 317 2.26e+01 d.14.1.5,d.58.26.3 72645,72646 1p7tA 731 2.29e+01 c.1.13.1 94319 1i7oA 429 2.31e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1cd9B 215 2.34e+01 1cto b.1.2.1,b.1.2.1 22041,22042 1q2bA 434 2.35e+01 b.29.1.10 95624 1ejfA 125 2.44e+01 1ejfA b.15.1.2 23683 1klfB 279 2.47e+01 b.2.3.2,b.2.3.2 72684,72685 1vhyA 257 2.50e+01 b.122.1.2,c.116.1.5 100714,100715 1uk8A 282 2.56e+01 c.69.1.10 107907 1n9pA 207 2.56e+01 b.1.18.16 80343 1amuA 563 2.58e+01 1amuA e.23.1.1 43351 1a02N 301 2.60e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 1f5fA 205 2.60e+01 1d2sA b.29.1.4 24222 1fsoA 139 2.68e+01 1rhoA b.1.18.8 60007 2gar 212 2.68e+01 2gar c.65.1.1 34161 1umkA 275 2.70e+01 1sz2A 332 2.76e+01 1zq1A 438 2.85e+01 1yxmA 303 2.91e+01 2b5oA 402 2.91e+01 6cel 434 3.00e+01 1celA b.29.1.10 24279 1k8kA 418 3.01e+01 c.55.1.1,c.55.1.1 68305,68306 1yacA 208 3.02e+01 1yacA c.33.1.3 31757 1z6mA 175 3.02e+01 1h7wA 1025 3.02e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 3aprE 325 3.04e+01 2er7E b.50.1.2 26820 1a0p 290 3.06e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 2bf6A 449 3.14e+01 1egnA 434 3.15e+01 1celA b.29.1.10 59411 1b7yB 785 3.15e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1iupA 282 3.19e+01 c.69.1.10 76815 2cxcA 144 3.19e+01 1kbpA 432 3.21e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 1v58A 241 3.21e+01 c.47.1.9,d.17.3.1 108371,108372 1dypA 271 3.24e+01 1dypA b.29.1.2 24185 1edg 380 3.25e+01 1edg c.1.8.3 28807 1w6sA 599 3.25e+01 1azsB 212 3.27e+01 1azsA d.58.29.1 39423 1noa 113 3.30e+01 2mcm b.1.7.1 22208 1zd9A 188 3.31e+01 2c2hA 192 3.32e+01 1azsA 220 3.37e+01 1azsA d.58.29.1 39416 1tx4B 178 3.37e+01 1ctqA c.37.1.8 32045 1xx0A 127 3.40e+01 1ci3M 249 3.41e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 1hynP 379 3.41e+01 1hynP d.112.1.2 61408 1w44A 331 3.43e+01 1hjsA 332 3.45e+01 c.1.8.3 83492 1umwA 237 3.47e+01 d.223.1.2,d.223.1.2 99631,99632 1jmxB 349 3.50e+01 b.69.2.2 66906 1vcbC 160 3.50e+01 1vcbC b.3.3.1 22535 1pv5A 264 3.54e+01 d.251.1.1 95150 1i0lA 221 3.59e+01 c.61.1.1 71096 1q18A 332 3.60e+01 c.55.1.7,c.55.1.7 104470,104471 2axcA 264 3.60e+01 2ajgA 196 3.71e+01 1i2aA 219 3.71e+01 e.24.1.1 90660 2apr 325 3.77e+01 2er7E b.50.1.2 26819 8acn 754 3.80e+01 1amj c.8.2.1,c.83.1.1 30724,35400 2a19A 175 3.84e+01 1a8y 367 3.85e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1i7pA 274 3.85e+01 b.43.4.2,c.25.1.1 66048,66049 1kmqA 184 3.87e+01 c.37.1.8 84412 1d2sA 170 3.87e+01 1d2sA b.29.1.4 24221 1w77A 228 3.92e+01 1gteA 1025 3.93e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1n2eA 300 4.02e+01 c.26.1.4 85268 1aerA 205 4.02e+01 1aerA d.166.1.1 42249 2f4lA 297 4.05e+01 1kid 203 4.06e+01 1derA c.8.5.1 30771 2apjA 260 4.21e+01 1eo9B 241 4.31e+01 3pchM b.3.6.1 22826 1lm4A 194 4.31e+01 d.167.1.1 84626 1mkaA 171 4.32e+01 1mkaA d.38.1.2 38543 1giqA 413 4.33e+01 d.166.1.1,d.166.1.1 76224,76225 1q25A 432 4.34e+01 b.64.1.1,b.64.1.1,b.64.1.1 104493,104494,104495 1b12A 248 4.36e+01 1b12A b.87.1.2 28388 1o0pA 104 4.41e+01 d.58.7.1 86535 1s5jA 847 4.47e+01 1bs4A 168 4.48e+01 1bs4A d.167.1.1 42287 1u4cA 349 4.50e+01 b.69.4.2 107666 2calA 154 4.50e+01 1n5nA 180 4.52e+01 d.167.1.1 85336 1nt2A 210 4.58e+01 c.66.1.3 86149 1zynA 202 4.59e+01 1e2wA 251 4.60e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1aun 208 4.62e+01 1thv b.25.1.1 23900 1qm4A 396 4.75e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1fc6A 388 4.79e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1iicA 422 4.81e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 2a1kA 233 4.94e+01 3psg 370 4.98e+01 1smrA b.50.1.2 26841 1tm9A 137 5.00e+01 a.225.1.1 107150 1dceA 567 5.00e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1e30A 155 5.03e+01 1rcy b.6.1.1 23016 2ewrA 170 5.15e+01 1vkfA 188 5.15e+01 c.1.29.1 108656 2phlA 397 5.17e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1feuA 206 5.18e+01 1feuA b.53.1.1 59801 1mdaH 368 5.19e+01 2bbkH b.69.2.1 27637 1vplA 256 5.21e+01 1ukkA 142 5.27e+01 d.227.1.1 99491 1qwiA 143 5.27e+01 d.227.1.1 96474 1oacA 727 5.33e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1zmdA 474 5.35e+01 1k20A 310 5.39e+01 c.107.1.1 68027 2cfuA 658 5.42e+01 2aa4A 289 5.45e+01 1pqhA 143 5.45e+01 b.52.2.1 95017 1grj 158 5.46e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1xodA 118 5.47e+01 1xeoA 168 5.51e+01 1z0sA 278 5.52e+01 1ghpA 258 5.58e+01 1btl e.3.1.1 60520 1jcfA 344 5.59e+01 c.55.1.1,c.55.1.1 62878,62879 1j8yF 297 5.64e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2bduA 297 5.66e+01 1wrjA 156 5.67e+01 1bupA 386 5.68e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1jkxA 212 5.69e+01 c.65.1.1 66813 2fbeA 201 5.79e+01 1nbaA 264 5.85e+01 1nbaA c.33.1.3 31753 1s1dA 331 5.86e+01 b.67.3.1 98344 1dkmA 410 5.90e+01 1dklA c.60.1.2 34000 1xfuA 747 5.91e+01 1k8kB 394 5.91e+01 c.55.1.1 68307 1m6iA 493 5.94e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 2b8lA 405 5.96e+01 1rcy 151 5.96e+01 1rcy b.6.1.1 23018 2bnfB 241 6.07e+01 1ja9A 274 6.14e+01 c.2.1.2 62817 1ogsA 497 6.17e+01 b.71.1.2,c.1.8.3 86997,86998 1qx4A 274 6.26e+01 b.43.4.2,c.25.1.1 104624,104625 1qunB 279 6.26e+01 b.2.3.2,b.2.3.2 22411,22412 1d3gA 367 6.32e+01 1d3gA c.1.4.1 28600 1j8rA 196 6.32e+01 1j8rA b.2.3.3 62745 1r8nA 185 6.38e+01 b.42.4.1 104851 1qqsA 174 6.40e+01 1nglA b.60.1.1 27143 1s8fA 177 6.41e+01 c.37.1.8 105370 2cygA 312 6.49e+01 1fonA 240 6.77e+01 5ptp b.47.1.2 26231 1z0nA 96 6.81e+01 2fclA 169 6.85e+01 2g0wA 296 6.85e+01 1ekjA 221 6.86e+01 1ekjB c.53.2.1 33364 1gpmA 525 6.87e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1hxhA 253 6.88e+01 c.2.1.2 76725 1prxA 224 6.89e+01 1prxA c.47.1.10 33076 1lml 478 6.91e+01 1lml d.92.1.3 40295 1voqa 90 7.01e+01 2bmoA 447 7.07e+01 1o7nB 194 7.08e+01 d.17.4.4 81164 1vhxA 150 7.08e+01 c.55.3.8 100712 1xzwA 426 7.11e+01 1bqbA 301 7.12e+01 1hyt d.92.1.2 58962 1ia9A 280 7.14e+01 1ia9A d.144.1.5 62113 1r17A 343 7.15e+01 b.2.3.4,b.2.3.4 96796,96797 1w4tA 299 7.15e+01 1dkuA 317 7.17e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1f6fB 210 7.18e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1q0qA 406 7.19e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1vdwA 254 7.24e+01 e.7.1.1 100569 2erfA 209 7.25e+01 1lbvA 252 7.25e+01 e.7.1.1 73813 1o5iA 249 7.32e+01 c.2.1.2 92499 1d02A 202 7.32e+01 1d02A c.52.1.8 33313 1eqcA 394 7.41e+01 1cz1A c.1.8.3 28811 1nnsA 326 7.44e+01 c.88.1.1 85910 1uteA 313 7.53e+01 1uteA d.159.1.1 42078 1x1nA 524 7.58e+01 1qwtA 255 7.59e+01 b.26.1.3 96501 1vjrA 271 7.64e+01 c.108.1.14 100832 1umdB 324 7.67e+01 c.36.1.7,c.48.1.2 99600,99601 1vm6A 228 7.69e+01 c.2.1.3,d.81.1.3 108876,108877 1kbvA 327 7.77e+01 b.6.1.3,b.6.1.3 68395,68396 1ygs 234 7.83e+01 1ygs b.26.1.1 23907 1ut1A 148 7.84e+01 b.2.3.6 108014 1kay 381 7.84e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1mo9A 523 7.90e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1cruA 454 7.91e+01 1c9uA b.68.2.1 27617 1gpc 218 7.92e+01 1gpc b.40.4.7 25393 1d0iA 156 7.95e+01 2dhqA c.23.13.1 31383 1u7nA 336 8.01e+01 c.77.1.4 107726 1xfxA 777 8.03e+01 1ek0A 170 8.09e+01 1ctqA c.37.1.8 32076 1u9aA 160 8.11e+01 1u9aA d.20.1.1 38333 1tib 269 8.11e+01 3tgl c.69.1.17 34738 1noyA 388 8.13e+01 1clqA c.55.3.5 33713 1t0qC 86 8.17e+01 d.15.12.1 106222 1dnv 437 8.17e+01 1dnv b.121.5.3 23332 1t3qB 788 8.20e+01 d.41.1.1,d.133.1.1 106369,106370 1pz7A 204 8.20e+01 b.29.1.4 95405 2cr4A 126 8.20e+01 2gjgA 248 8.20e+01 1v1aA 309 8.20e+01 c.72.1.1 100249 1v5wA 343 8.20e+01 c.37.1.11 108387 1li5B 461 8.22e+01 a.27.1.1,c.26.1.1 73914,73915 2madH 373 8.24e+01 2bbkH b.69.2.1 27639 1s6lA 212 8.26e+01 1mkyA 439 8.30e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1z0mA 96 8.35e+01 2a6tA 271 8.35e+01 2sicI 107 8.40e+01 3ssi d.84.1.1 40031 1uz5A 402 8.45e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1dkqA 410 8.45e+01 1dklA c.60.1.2 33998 1ftrA 296 8.45e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1vr1H 261 8.45e+01 5ptp 1ospO 257 8.47e+01 1ospO b.76.1.1 27971 1sqrA 95 8.54e+01 2c0zA 216 8.62e+01 7taa 478 8.64e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1r3eA 309 8.65e+01 b.122.1.1,d.265.1.2 96907,96908 1widA 130 8.66e+01 1aisB 200 8.66e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1qwdA 177 8.71e+01 b.60.1.1 96471 1kmtA 141 8.71e+01 b.1.18.8 77442 1x82A 190 8.72e+01 1avbA 226 8.72e+01 1led b.29.1.1 24158 1w96A 554 8.72e+01 1bkb 136 8.77e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1vqoX 92 8.78e+01 1oxdA 227 8.78e+01 d.22.1.1 93687 1yrtA 364 8.78e+01 1wnhA 225 8.81e+01 1n4xH 120 8.89e+01 b.1.1.1 85324 1wkaA 147 8.90e+01