# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 1e0tA 470 2.74e-02 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1v7lA 163 3.42e-02 1xneA 113 5.41e-02 2gp4A 628 8.47e-02 1xe1A 116 1.11e-01 b.43.3.1 109571 2hcuA 213 1.16e-01 1wsrA 375 1.55e-01 1ofdA 1520 1.59e-01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1vkyA 347 2.01e-01 e.53.1.1 108696 1r6xA 395 2.07e-01 b.122.1.3,c.26.1.5 97167,97168 1o54A 277 2.34e-01 c.66.1.13 92482 1te7A 103 2.98e-01 2g50A 530 3.35e-01 2g1lA 104 3.64e-01 1w44A 331 4.15e-01 3ullA 132 4.76e-01 3ullA b.40.4.3 25282 1cv8 174 5.16e-01 1cv8 d.3.1.1 37089 1t2wA 145 6.05e-01 b.100.1.1 106289 1wocA 103 6.15e-01 1ckmA 330 7.56e-01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1ugpB 226 8.10e-01 b.34.4.4 107832 1bkb 136 9.47e-01 1bkb b.34.5.2,b.40.4.5 24609,25341 1a34A 159 1.08e+00 1a34A b.121.7.1 23286 1x3eA 165 1.18e+00 1zeqX 84 1.24e+00 2napA 723 1.25e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1b9mA 265 1.29e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2as9A 210 1.29e+00 2ha8A 184 1.41e+00 1gzcA 239 1.49e+00 b.29.1.1 70803 1kblA 873 1.51e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1qvcA 145 1.51e+00 3ullA b.40.4.3 25284 1uebA 184 1.51e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1kzlA 208 1.60e+00 b.43.4.3,b.43.4.3 77635,77636 1yavA 159 1.62e+00 1wosA 364 1.63e+00 b.44.2.1,d.250.1.1 109468,109469 1wfwA 74 1.69e+00 1g2bA 62 1.74e+00 1tud b.34.2.1 24488 1gweA 503 1.94e+00 e.5.1.1 70667 1yn8A 59 1.96e+00 1pqhA 143 2.08e+00 b.52.2.1 95017 1iz6A 138 2.14e+00 b.34.5.2,b.40.4.5 76976,76977 1jnyA 435 2.14e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1xm8A 254 2.21e+00 1sv6A 269 2.32e+00 d.177.1.1 106043 1im3D 95 2.37e+00 1im3D b.1.18.5 62568 2f9hA 129 2.40e+00 1x6oA 174 2.44e+00 b.34.5.2,b.40.4.5 109493,109494 1wmmA 145 2.45e+00 1sbyA 254 2.57e+00 1ooeA 236 2.57e+00 c.2.1.2 87196 2asbA 251 2.65e+00 1q7eA 428 2.99e+00 c.123.1.1 96035 2gjgA 248 3.09e+00 1yueA 427 3.14e+00 1pht 85 3.18e+00 1ckaA b.34.2.1 24483 1ijaA 148 3.23e+00 1ijaA b.100.1.1 62484 1lo7A 141 3.23e+00 d.38.1.1 74144 1r3eA 309 3.58e+00 b.122.1.1,d.265.1.2 96907,96908 2gu2A 312 3.60e+00 1pxfA 111 3.66e+00 b.40.4.4 88341 1qcsA 211 3.77e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1wruA 379 3.77e+00 1z47A 355 3.83e+00 1pj5A 830 3.98e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1qwlA 505 4.00e+00 e.5.1.1 96483 1zkoA 136 4.01e+00 1zymA 258 4.01e+00 1zymA a.60.10.1,c.8.1.2 18110,30705 1mg4A 113 4.07e+00 d.15.11.1 84953 2b7nA 273 4.07e+00 1z6bA 154 4.09e+00 1owfA 99 4.16e+00 a.55.1.1 87487 1k4iA 233 4.36e+00 d.115.1.2 72056 1q7hA 153 4.41e+00 b.122.1.1,d.17.6.2 96042,96043 1ybiA 288 4.48e+00 1am2 199 4.48e+00 1am2 b.86.1.2 28381 1tig 94 4.78e+00 1tig d.68.1.1 39566 1obbA 480 4.83e+00 c.2.1.5,d.162.1.2 86760,86761 1w70A 60 4.84e+00 2eulA 156 4.90e+00 1b34B 118 5.06e+00 1b34B b.38.1.1 24797 1h0hA 977 5.18e+00 b.52.2.2,c.81.1.1 76435,76436 2cbp 96 5.20e+00 2cbp b.6.1.1 22895 1v5vA 401 5.33e+00 1nkqA 259 5.36e+00 d.177.1.1 103862 2g6fX 59 5.38e+00 2b5hA 200 5.43e+00 1kqfA 1015 5.64e+00 b.52.2.2,c.81.1.1 72871,72872 2fxqA 264 5.66e+00 1kk1A 410 5.66e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1oi2A 366 5.80e+00 c.119.1.2 103802 1gttA 429 5.94e+00 d.177.1.1,d.177.1.1 70529,70530 2gfaA 119 5.96e+00 1up7A 417 5.98e+00 2f1rA 171 6.00e+00 1h9mA 145 6.02e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 2bi0A 337 6.06e+00 1y8qB 640 6.09e+00 2ltnA 181 6.22e+00 1led b.29.1.1 24024 1z54A 132 6.31e+00 1y0nA 78 6.35e+00 1i8dA 213 6.36e+00 b.43.4.3,b.43.4.3 61953,61954 1tksA 204 6.36e+00 d.115.1.2 107114 1vajA 214 6.48e+00 1jg1A 235 6.70e+00 c.66.1.7 66661 2eveA 157 6.77e+00 2an1A 292 6.79e+00 1f60A 458 6.82e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2gcuA 245 6.86e+00 1vi4A 174 6.94e+00 c.8.7.1 100731 1zh1A 163 6.96e+00 1whi 122 7.00e+00 1whi b.39.1.1 24810 1sawA 225 7.21e+00 2crvA 120 7.35e+00 1pk6A 133 7.53e+00 b.22.1.1 94801 1qauA 112 7.61e+00 1qauA b.36.1.1 24779 1i1jA 108 7.70e+00 1i1jA b.34.2.1 61531 1i7dA 659 7.73e+00 1d6mA e.10.1.1 61886 1lgpA 116 7.82e+00 b.26.1.2 73890 2bhoA 130 8.04e+00 1dzfA 215 8.16e+00 1dzfA c.52.3.1,d.78.1.1 33344,39753 1wgsA 133 8.22e+00 2fbyA 205 8.25e+00 2ff4A 388 8.29e+00 2bgiA 272 8.45e+00 1zceA 155 8.53e+00 1pmi 440 8.56e+00 1pmi b.82.1.3 28114 2tnfA 156 8.57e+00 2tnfA b.22.1.1 23880 1aiw 62 8.65e+00 1aiw b.72.2.1 27808 1dvoA 152 9.11e+00 1dvoA a.136.1.1 19623 1si2A 149 9.18e+00 b.34.14.1 105569 1g6gA 127 9.39e+00 1g6gA b.26.1.2 23916 1xjjA 644 9.52e+00 1m7sA 484 9.75e+00 e.5.1.1 74574 1pl8A 356 9.82e+00 b.35.1.2,c.2.1.1 94878,94879 1suuA 312 9.92e+00 b.68.10.1 99006 2h1rA 299 9.93e+00 1pch 88 9.97e+00 1ptf d.94.1.1 40564 1gcqC 70 1.00e+01 1gcpA b.34.2.1 60436 1winA 143 1.00e+01 1twfF 155 1.00e+01 1gcqA 61 1.02e+01 1ckaA b.34.2.1 60434 1hyoA 421 1.02e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1vc3B 97 1.05e+01 1t5hX 504 1.05e+01 e.23.1.1 106449 1oruA 195 1.07e+01 b.58.1.2 93464 1wdtA 665 1.07e+01 1rqwA 207 1.08e+01 b.25.1.1 97781 1okgA 373 1.10e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1vzqH 250 1.10e+01 1ckaA 57 1.12e+01 1ckaA b.34.2.1 24459 1yduA 170 1.13e+01 1z3qA 200 1.15e+01 1v8bA 479 1.19e+01 1kwgA 645 1.22e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1i9gA 280 1.22e+01 c.66.1.13 62090 1tt7A 330 1.22e+01 1ju3A 583 1.25e+01 b.18.1.13,c.69.1.21 67300,67301 1zlmA 58 1.25e+01 1q5xA 161 1.26e+01 c.8.7.1 95947 1zud2 66 1.26e+01 1li4A 432 1.28e+01 c.2.1.4,c.23.12.3 84616,84617 2g7iA 125 1.28e+01 1vpjA 192 1.28e+01 1eu3A 210 1.29e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 2bpa1 426 1.31e+01 2bpa1 2brfA 110 1.32e+01 1ixlA 131 1.33e+01 d.38.1.5 90717 1smxA 96 1.33e+01 b.40.4.5 105772 2hglA 136 1.34e+01 1hr0W 71 1.34e+01 1ah9 b.40.4.5 25329 1uwfA 158 1.34e+01 1ruwA 69 1.36e+01 1x82A 190 1.37e+01 1rocA 155 1.37e+01 b.1.22.1 97673 1fxkC 133 1.39e+01 1fxkC a.2.5.1 15702 1xffA 240 1.40e+01 d.153.1.1 109580 1uedA 406 1.43e+01 a.104.1.1 99256 1c96A 753 1.51e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1w94A 156 1.56e+01 1zq9A 285 1.57e+01 1x74A 360 1.58e+01 1rz2A 254 1.58e+01 b.100.1.1 105130 1jsdA 319 1.59e+01 b.19.1.2 63258 1sacA 204 1.61e+01 1sacA b.29.1.5 24237 1o7iA 119 1.61e+01 b.40.4.3 86642 1oj5A 132 1.61e+01 d.110.3.8 93087 1o6aA 96 1.62e+01 b.139.1.1 92562 2fcfA 103 1.63e+01 2a6pA 208 1.63e+01 1fvuB 125 1.64e+01 1ixxB d.169.1.1 42346 1l2tA 235 1.64e+01 c.37.1.12 73514 1tovA 98 1.66e+01 b.34.10.1 107179 1ew4A 106 1.66e+01 1ew4A d.82.2.1 40023 2c1xA 456 1.68e+01 2evrA 246 1.68e+01 1snnA 227 1.71e+01 d.115.1.2 105821 1f3lA 321 1.75e+01 1g6q2 c.66.1.6 59630 1lam 484 1.75e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1t3yA 141 1.76e+01 1r77A 103 1.78e+01 1mixA 206 1.79e+01 a.11.2.1,b.55.1.5 79166,79167 1uj0A 62 1.79e+01 b.34.2.1 99449 2ar1A 172 1.80e+01 1erjA 393 1.80e+01 1erjA b.69.4.1 27660 2cf8H 257 1.81e+01 1eylA 186 1.81e+01 1wba b.42.4.1 25593 1ng2A 193 1.82e+01 b.34.2.1,b.34.2.1 85660,85661 1zjkA 403 1.82e+01 1sgoA 139 1.82e+01 d.82.3.1 98857 2furA 209 1.83e+01 1pl4A 198 1.83e+01 a.2.11.1,d.44.1.1 94854,94855 1y43B 173 1.83e+01 2h4uA 145 1.85e+01 1z85A 234 1.85e+01 1wlyA 333 1.85e+01 1ojrA 274 1.86e+01 c.74.1.1 93147 1vkkA 154 1.86e+01 d.109.1.2 108669 1zx8A 136 1.86e+01 1h8dH 260 1.87e+01 5ptp 1pvl 301 1.88e+01 1pvl f.6.1.1 43819 1bdmA 327 1.92e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1k5cA 335 1.92e+01 b.80.1.3 72076 1fmtA 314 1.95e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2a6sA 84 1.96e+01 1zl0A 311 1.96e+01 2bsjA 133 1.96e+01 1a1x 108 1.96e+01 1a1x b.63.1.1 27514 2as0A 396 1.97e+01 2bnuA 203 1.98e+01 1se8A 301 1.98e+01 b.40.4.3 105448 1whzA 70 1.99e+01 2c3nA 247 2.00e+01 1svvA 359 2.01e+01 c.67.1.1 106054 1uufA 369 2.02e+01 b.35.1.2,c.2.1.1 100006,100007 2blnA 305 2.02e+01 2gf6A 135 2.02e+01 1gppA 237 2.04e+01 b.86.1.2 76262 1ve0A 134 2.05e+01 1rfs 139 2.06e+01 1rfs b.33.1.1 24434 1y8oB 128 2.08e+01 1k07A 263 2.09e+01 d.157.1.1 77218 1uy4A 145 2.12e+01 b.18.1.10 108131 1wzoA 246 2.17e+01 1oacA 727 2.18e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1cqxA 403 2.18e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1uf3A 228 2.20e+01 d.159.1.6 99317 2bw2A 140 2.22e+01 1t61C 227 2.23e+01 d.169.1.6,d.169.1.6 106533,106534 1b12A 248 2.23e+01 1b12A b.87.1.2 28388 1gxrA 337 2.23e+01 b.69.4.1 70722 1k8wA 327 2.23e+01 b.122.1.1,d.265.1.2 83094,90388 1gvhA 396 2.24e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1uwwA 191 2.24e+01 b.18.1.23 108079 1owfB 94 2.26e+01 a.55.1.1 87488 1yqdA 366 2.26e+01 2b9sB 62 2.29e+01 1ws8A 109 2.30e+01 1vm9A 111 2.31e+01 b.33.1.1 108886 1wp5A 323 2.33e+01 1sr8A 298 2.35e+01 e.54.1.1 105959 2gs5A 198 2.35e+01 1yp5A 58 2.36e+01 1gs5A 258 2.36e+01 c.73.1.2 70395 1yoxA 250 2.36e+01 1wn2A 121 2.40e+01 1vs0A 310 2.41e+01 2bhgA 209 2.43e+01 2d8aA 348 2.43e+01 1euwA 152 2.45e+01 1dupA b.85.4.1 28349 1y9aA 360 2.46e+01 2a8eA 220 2.46e+01 1g291 372 2.48e+01 1g291 2cwzA 141 2.48e+01 1dcjA 81 2.50e+01 1dcjA d.68.3.3 59115 1v8qA 85 2.51e+01 b.84.4.1 108428 1i1nA 226 2.52e+01 c.66.1.7 71102 1iq8A 582 2.55e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2czlA 272 2.55e+01 2cyeA 133 2.55e+01 1e0bA 68 2.57e+01 1e0bA b.34.13.2 37476 2db1A 118 2.59e+01 1jsmA 325 2.63e+01 b.19.1.2 63264 1uwzA 136 2.63e+01 c.97.1.1 108081 1zdyA 307 2.65e+01 2ck3A 510 2.65e+01 1g4fA 86 2.65e+01 1qubA g.18.1.1 44873 1k4mA 213 2.69e+01 c.26.1.3 77258 2cvdA 198 2.70e+01 1tw9A 206 2.71e+01 a.45.1.1,c.47.1.5 107381,107382 2fbwA 621 2.71e+01 1gtmA 419 2.72e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1a62 130 2.72e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1mxgA 435 2.72e+01 b.71.1.1,c.1.8.1 85193,85194 1shfA 59 2.74e+01 1bbzA b.34.2.1 24462 1sixA 174 2.75e+01 b.85.4.1 98892 1mhnA 59 2.75e+01 b.34.9.1 84964 2gnqA 336 2.75e+01 1elvA 333 2.76e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1cewI 108 2.76e+01 1cewI d.17.1.2 37999 1rcqA 357 2.80e+01 b.49.2.2,c.1.6.1 104882,104883 1lfkA 398 2.81e+01 a.104.1.1 77926 1w9aA 147 2.82e+01 1jo8A 58 2.84e+01 b.34.2.1 71774 2gdzA 267 2.87e+01 1uz8B 212 2.88e+01 b.1.1.1,b.1.1.2 108168,108169 1ym3A 215 2.88e+01 2eifA 136 2.88e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2c2aA 258 2.88e+01 1r9hA 135 2.89e+01 d.26.1.1 97260 1l1eA 287 2.93e+01 c.66.1.18 73454 1w4sA 174 2.94e+01 1ro0A 216 2.95e+01 d.264.1.2 97664 1m1zA 513 2.96e+01 c.26.2.1,d.153.1.1 78457,78458 1g5cA 170 2.97e+01 1g5cA c.53.2.1 60264 1pueE 89 2.97e+01 1awcA a.4.5.21 16165 1vqoS 85 2.98e+01 1iyhA 198 2.99e+01 a.45.1.1,c.47.1.5 83790,83791 1wdiA 345 3.04e+01 1hl9A 449 3.05e+01 b.71.1.3,c.1.8.11 90650,90651 2fytA 340 3.06e+01 1jztA 246 3.06e+01 c.104.1.1 63319 1je5A 206 3.08e+01 1je5A b.40.4.7 62909 2bynA 227 3.09e+01 1nw3A 416 3.10e+01 c.66.1.31 86288 1ssxA 198 3.11e+01 b.47.1.1 98978 1ia9A 280 3.14e+01 1ia9A d.144.1.5 62113 1j8rA 196 3.14e+01 1j8rA b.2.3.3 62745 2h14A 317 3.15e+01 1ve2A 235 3.15e+01 1v37A 177 3.16e+01 1w1hA 151 3.17e+01 1xovA 326 3.18e+01 1vj2A 126 3.20e+01 b.82.1.10 100796 1i12A 160 3.22e+01 1i21A d.108.1.1 61515 2czsA 80 3.22e+01 2aneA 125 3.23e+01 1eaqA 140 3.26e+01 b.2.5.6 76144 1m4jA 142 3.27e+01 d.109.1.2 78602 1ok8A 394 3.28e+01 b.1.18.4,f.10.1.1 93236,93237 1o57A 291 3.29e+01 a.4.5.40,c.61.1.1 92483,92484 1yliA 153 3.30e+01 1uxxX 133 3.30e+01 b.18.1.10 100169 1c93A 265 3.32e+01 2ebn c.1.8.5 28998 2fk8A 318 3.34e+01 2sga 181 3.35e+01 1qq4A b.47.1.1 25808 1h2eA 207 3.36e+01 c.60.1.1 70857 1x6zA 123 3.37e+01 2cx7A 130 3.38e+01 1kwmA 402 3.38e+01 c.56.5.1,d.58.3.1 73079,73080 1s98A 107 3.42e+01 b.124.1.1 105377 1z5bA 469 3.42e+01 1aa6 715 3.45e+01 2napA b.52.2.2,c.81.1.1 26916,35324 2calA 154 3.46e+01 1mai 131 3.46e+01 1mai b.55.1.1 26951 1r71A 178 3.56e+01 a.4.14.1 104823 1yxyA 234 3.57e+01 2b06A 155 3.59e+01 2g7uA 257 3.64e+01 1gd7A 109 3.66e+01 b.40.4.4 60441 1jb0D 138 3.70e+01 1jb0D d.187.1.1 62823 1bli 483 3.70e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1m2tA 254 3.77e+01 d.165.1.1 84761 2b5iD 217 3.78e+01 1eq2A 310 3.79e+01 1eq2A c.2.1.2 29814 1k3yA 221 3.82e+01 a.45.1.1,c.47.1.5 77245,77246 2a50A 73 3.83e+01 1fljA 260 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