# List of top-scoring protein chains for t04-100-30-o_sep-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 1itcA 516 2.85e-01 b.3.1.1,c.1.8.1 83705,83706 1vemA 516 3.90e-01 1k0wA 231 7.11e-01 c.74.1.1 77220 1din 236 7.27e-01 1din c.69.1.9 34682 1kshA 186 8.83e-01 c.37.1.8 72914 2agyA 361 9.02e-01 1zi8A 236 1.25e+00 1n0nA 199 1.67e+00 a.2.11.1,d.44.1.1 79750,79751 1pl4A 198 1.87e+00 a.2.11.1,d.44.1.1 94854,94855 1ap6A 198 2.01e+00 1avmA a.2.11.1,d.44.1.1 15746,38705 1yyaA 250 2.58e+00 1io1A 398 2.84e+00 1io1A e.32.1.1 62611 1wjxA 122 2.98e+00 1nar 290 3.32e+00 1nar c.1.8.5 28988 2gnqA 336 3.45e+00 1nrfA 262 3.51e+00 e.3.1.1 92086 1q15A 503 3.72e+00 c.26.2.1,d.153.1.1 95538,95539 2gu3A 136 4.33e+00 1sfxA 109 4.49e+00 a.4.5.50 105505 1sh0A 510 4.51e+00 e.8.1.4 98876 1obdA 306 5.25e+00 d.143.1.1 86767 1nmoA 247 5.31e+00 c.135.1.1 91980 1q0xH 221 5.92e+00 b.1.1.1,b.1.1.2 95517,95518 4icb 76 5.93e+00 4icb a.39.1.1 17145 2a5dA 175 6.09e+00 1hdmA 201 6.11e+00 1iakA b.1.1.2,d.19.1.1 21583,38157 1ig5A 75 6.28e+00 4icb a.39.1.1 62363 2cblA 305 6.28e+00 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1iicA 422 6.29e+00 1nmtA d.108.1.2,d.108.1.2 62422,62423 1w3jA 468 6.32e+00 c.1.8.4 109156 1uw4A 91 6.70e+00 d.58.7.4 100071 1h49A 512 7.06e+00 c.1.8.4 83477 1g5bA 221 7.29e+00 1g5bA d.159.1.3 60261 2cnqA 306 7.39e+00 1zkjA 359 7.42e+00 1lci 550 7.54e+00 1lci e.23.1.1 43349 1yvhA 329 7.89e+00 1rypL 212 7.94e+00 d.153.1.4 41880 1wmhA 89 8.27e+00 1a48 306 8.31e+00 1a48 d.143.1.1 41590 1rypJ 204 8.32e+00 d.153.1.4 41878 1mr3F 181 8.32e+00 c.37.1.8 79422 1o50A 157 8.48e+00 d.37.1.1,d.37.1.1 92478,92479 2bkdN 134 8.52e+00 1aerA 205 8.53e+00 1aerA d.166.1.1 42249 2acaA 189 9.37e+00 1v02A 565 9.44e+00 c.1.8.4 108194 1yadA 221 9.58e+00 2b43A 526 9.73e+00 1f9zA 135 9.74e+00 1qipA d.32.1.1 38484 2b30A 301 9.75e+00 2breA 219 1.00e+01 1ghpA 258 1.00e+01 1btl e.3.1.1 60520 1mg4A 113 1.03e+01 d.15.11.1 84953 2agcA 162 1.06e+01 1h4rA 314 1.06e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1yumA 242 1.10e+01 1e55A 512 1.12e+01 1e70M c.1.8.4 28934 1zd9A 188 1.12e+01 1oo0A 147 1.15e+01 d.232.1.1 87182 1garA 212 1.16e+01 2gar c.65.1.1 34162 1l6oA 95 1.16e+01 b.36.1.1 84534 1ywnA 316 1.19e+01 1jlyA 304 1.20e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1exbA 332 1.22e+01 1qrqA c.1.7.1 28666 1nvpD 108 1.25e+01 a.32.1.1,b.56.1.1 92213,92214 1bb8 71 1.27e+01 2bb8 d.10.1.1 37478 1gx5A 536 1.29e+01 e.8.1.4 70682 1q42A 201 1.30e+01 d.17.4.2 95776 2fsrA 195 1.36e+01 1mg7A 417 1.36e+01 d.14.1.6,d.58.26.6 84954,84955 1zx8A 136 1.37e+01 2brcA 214 1.38e+01 1y1uA 585 1.39e+01 1fa8A 135 1.43e+01 1qipA d.32.1.1 38486 1o3yA 166 1.45e+01 c.37.1.8 86618 2b6hA 192 1.47e+01 1yh6A 179 1.47e+01 1zarA 282 1.48e+01 1wdyA 285 1.50e+01 1a8y 367 1.51e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1hurA 180 1.53e+01 1hurA c.37.1.8 32052 2f9dA 125 1.53e+01 2fckA 181 1.54e+01 1c2pA 576 1.55e+01 1quvA e.8.1.4 43117 1tqmA 282 1.55e+01 a.4.5.56,d.144.1.9 107236,107237 1ikpA 613 1.56e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2cz1A 206 1.57e+01 2cfaA 217 1.60e+01 2cbuA 468 1.60e+01 1tw4A 125 1.63e+01 1k0sA 151 1.69e+01 b.40.7.1 67969 2btvA 901 1.73e+01 2btvA e.28.1.1 43376 1jkxA 212 1.74e+01 c.65.1.1 66813 1o4rA 108 1.74e+01 d.93.1.1 92469 1b35B 255 1.74e+01 1b35B b.121.4.1 23334 1cojA 212 1.77e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2b7kA 200 1.79e+01 1f6bA 198 1.85e+01 c.37.1.8 64986 1khiA 176 1.87e+01 b.34.5.2,b.40.4.5 77408,77409 1ab4 477 1.87e+01 1ab4 e.11.1.1 43251 1v5sA 126 1.88e+01 d.129.6.1 108384 1yrvA 169 1.89e+01 1xahA 354 1.91e+01 1f35A 162 1.92e+01 1f35A b.94.1.1 59628 2ajgA 196 1.92e+01 1lm6A 215 1.92e+01 d.167.1.1 84628 1vjeA 166 1.92e+01 d.185.1.2 100807 1r29A 127 1.94e+01 d.42.1.1 96856 1nteA 82 2.03e+01 b.36.1.1 86163 2fz4A 237 2.04e+01 2f1kA 279 2.06e+01 1uwcA 261 2.10e+01 c.69.1.17 100101 1ah6 220 2.12e+01 1yer d.122.1.1 41094 1uurA 473 2.13e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1shbA 104 2.16e+01 1fmk d.93.1.1 40425 1j7lA 264 2.19e+01 d.144.1.6 62697 2fg9A 178 2.23e+01 1p4kA 295 2.23e+01 d.153.1.5 87772 1th0A 226 2.24e+01 d.3.1.7 106903 2c1iA 431 2.25e+01 1zsxA 347 2.28e+01 1tib 269 2.28e+01 3tgl c.69.1.17 34738 1osdA 72 2.31e+01 d.58.17.1 104022 1h6lA 353 2.35e+01 b.68.3.1 60687 1ih8A 271 2.38e+01 2nsyA c.26.2.1 62377 1zhvA 134 2.38e+01 1irsA 112 2.40e+01 1qqgA b.55.1.2 26991 1zm8A 259 2.40e+01 2ftbA 125 2.40e+01 1j55A 95 2.41e+01 a.39.1.2 77078 1btl 263 2.43e+01 1btl e.3.1.1 42691 1v58A 241 2.44e+01 c.47.1.9,d.17.3.1 108371,108372 1rpyA 114 2.46e+01 d.93.1.1 97718 1wwzA 159 2.46e+01 2a0jA 149 2.48e+01 1ylhA 560 2.48e+01 1yw4A 341 2.50e+01 1g8yA 279 2.52e+01 1g8yA c.37.1.11 32302 1n0qA 93 2.55e+01 k.37.1.1 79754 1l2lA 457 2.56e+01 c.72.1.3 77656 1xa1A 255 2.58e+01 e.3.1.1 109529 1lv7A 257 2.60e+01 c.37.1.20 78232 1p6pA 125 2.61e+01 b.60.1.2 87839 1e44B 96 2.65e+01 1e44B b.101.1.1 59220 2pooA 355 2.66e+01 1qlgA b.68.3.1 27626 1mml 265 2.68e+01 1mml e.8.1.2 43015 1krs 120 2.68e+01 1krs b.40.4.1 25256 2aieP 203 2.72e+01 2cn3A 737 2.75e+01 1ri6A 343 2.76e+01 b.69.11.1 97503 1ru0A 105 2.76e+01 1th8A 145 2.79e+01 d.122.1.3 106908 2basA 431 2.81e+01 2f0aA 98 2.82e+01 1r8sA 164 2.83e+01 c.37.1.8 97247 1yfnA 118 2.86e+01 1qfxA 460 2.87e+01 1qfxA c.60.1.2 33994 1t2jA 116 2.87e+01 1vqoS 85 2.90e+01 1xs1A 193 2.91e+01 1fj2A 232 2.92e+01 1auoA c.69.1.14 34720 2b20A 403 2.93e+01 1nrjA 158 2.94e+01 d.110.4.4 86124 1ufwA 95 2.97e+01 d.58.7.1 99358 1xcbA 211 2.98e+01 a.4.5.38,c.2.1.12 109552,109553 1wzvA 155 2.98e+01 1pbgA 468 3.02e+01 1e70M c.1.8.4 28946 1seiA 130 3.03e+01 1seiA d.140.1.1 41463 2agaA 190 3.03e+01 1bf5A 545 3.06e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 9gafA 295 3.09e+01 1apyA d.153.1.5 42008 2cw8A 537 3.09e+01 1xkzA 255 3.10e+01 1azo 232 3.11e+01 1azo c.52.1.14 33329 1dfcA 493 3.12e+01 1dfcA b.42.5.1,b.42.5.1,b.42.5.1,b.42.5.1 25616,25617,25618,25619 2c1gA 431 3.12e+01 1hskA 326 3.16e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1zj6A 187 3.17e+01 1zy9A 564 3.18e+01 1a4pA 96 3.18e+01 1b4cA a.39.1.2 17176 1sqsA 242 3.19e+01 c.23.5.5 98968 1vgwA 231 3.19e+01 c.68.1.13 100612 1zyiA 171 3.20e+01 1rcqA 357 3.23e+01 b.49.2.2,c.1.6.1 104882,104883 1kveB 77 3.25e+01 1kveB 1sxrA 183 3.25e+01 d.118.1.1 106101 1i2sA 282 3.25e+01 e.3.1.1 71104 1gt6A 269 3.28e+01 c.69.1.17 76342 1ny9A 143 3.30e+01 a.181.1.1 86401 2gwnA 452 3.33e+01 1innA 166 3.34e+01 1j98A d.185.1.2 62608 1nzjA 298 3.37e+01 c.26.1.1 92377 1wrvA 308 3.37e+01 1fdr 248 3.40e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2ervA 150 3.42e+01 1q33A 292 3.44e+01 d.113.1.1 95657 4pgaA 337 3.44e+01 4pgaA c.88.1.1 35565 1y71A 130 3.47e+01 1yc9A 442 3.48e+01 1nnsA 326 3.48e+01 c.88.1.1 85910 1to4A 156 3.50e+01 b.1.8.1 107162 1g13A 162 3.51e+01 1g13A b.95.1.1 60194 1r6jA 82 3.54e+01 b.36.1.1 97151 1ycdA 243 3.54e+01 1y8qA 346 3.55e+01 1pu5A 164 3.61e+01 b.95.1.1 104310 1i3zA 103 3.62e+01 d.93.1.1 83667 1w2fA 276 3.67e+01 d.143.1.3 109125 2bkyA 97 3.68e+01 1smoA 119 3.71e+01 b.1.1.1 105764 1k2yX 463 3.72e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2cb2A 318 3.72e+01 1rypF 233 3.73e+01 1rypF d.153.1.4 41937 1txdA 385 3.74e+01 a.87.1.1,b.55.1.1 107422,107423 1jiwI 106 3.75e+01 1smpI b.61.2.1 63078 1m22A 503 3.76e+01 c.117.1.1 78464 1zt2B 212 3.76e+01 2ahjA 206 3.78e+01 2ahjA d.149.1.1 41772 2ex0A 399 3.78e+01 1vmbA 140 3.80e+01 2aexA 346 3.89e+01 2gar 212 3.89e+01 2gar c.65.1.1 34161 1oa8A 133 3.92e+01 b.145.1.1 92698 1zelA 298 3.93e+01 2czrA 226 3.94e+01 2ag9A 164 3.99e+01 2bkkA 264 4.01e+01 1g2iA 166 4.01e+01 1g2iA c.23.16.2 31438 1nlfA 279 4.02e+01 c.37.1.11 85850 1s5jA 847 4.08e+01 2ag4A 164 4.12e+01 1o17A 345 4.14e+01 a.46.2.1,c.27.1.1 80765,80766 1k5dB 201 4.16e+01 b.55.1.3 68169 1rxdA 159 4.16e+01 2dg5B 190 4.17e+01 4blmA 265 4.18e+01 1btl e.3.1.1 42721 2b7eA 59 4.20e+01 1g2yA 32 4.21e+01 a.34.2.1 17003 1tfzA 424 4.23e+01 d.32.1.3,d.32.1.3 106886,106887 1h9oA 112 4.23e+01 1qadA d.93.1.1 60837 1m40A 263 4.27e+01 e.3.1.1 74437 1h0xA 100 4.27e+01 d.68.6.1 76451 1pcfA 66 4.28e+01 1pcfA d.18.1.1 38142 1nqkA 381 4.30e+01 c.1.16.4 92050 1uylA 236 4.31e+01 d.122.1.1 108147 1sqrA 95 4.35e+01 1kqpA 271 4.35e+01 c.26.2.1 72883 1s99A 200 4.36e+01 1deuA 277 4.38e+01 1theB d.3.1.1 37085 2gaiA 633 4.39e+01 2bvfA 459 4.40e+01 2gkpA 167 4.41e+01 1g291 372 4.43e+01 1g291 2fa8A 105 4.43e+01 1t92A 116 4.45e+01 1gxuA 91 4.45e+01 d.58.10.1 76378 2b3yA 888 4.46e+01 1jltA 122 4.46e+01 a.133.1.2 66867 1crzA 403 4.47e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1d8wA 426 4.50e+01 1de5A c.1.15.2 29394 1htjF 210 4.54e+01 1htjF a.91.1.1 61254 1zckA 154 4.55e+01 1qmeA 702 4.55e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1tvoA 368 4.59e+01 1bylA 125 4.59e+01 1bylA d.32.1.2 38495 1x0vA 354 4.67e+01 1xniA 118 4.72e+01 1ru3A 732 4.73e+01 e.26.1.3 97835 3erk 364 4.74e+01 1hcl d.144.1.7 41654 1q4rA 112 4.75e+01 d.58.4.4 95823 2bbkL 125 4.75e+01 2bbkL g.21.1.1 44882 1sqjA 789 4.77e+01 b.69.13.1,b.69.13.1 105918,105919 2atrA 138 4.78e+01 2h17A 181 4.79e+01 1kolA 398 4.80e+01 b.35.1.2,c.2.1.1 77474,77475 2bngA 149 4.80e+01 1mbe 53 4.89e+01 1mbe a.4.1.3 16038 1t1gA 364 4.92e+01 c.41.1.2 106246 1s7hA 200 4.95e+01 d.58.48.2 105349 1htwA 158 4.97e+01 c.37.1.18 71083 1x3pA 54 4.97e+01 1kutA 230 4.98e+01 d.143.1.1 73017 2aumA 317 5.00e+01 1em8A 147 5.00e+01 c.128.1.1 90457 1uz1A 468 5.02e+01 1c4rA 182 5.06e+01 1c4rA b.29.1.4 24229 1zrsA 317 5.06e+01 1uv4A 293 5.07e+01 2d2jA 329 5.07e+01 1zl0A 311 5.08e+01 1k1aA 241 5.09e+01 d.211.1.1 67992 1r0vA 305 5.11e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2fpoA 202 5.13e+01 2aclB 244 5.13e+01 1dbqA 289 5.13e+01 1qpzA c.93.1.1 35666 2gfaA 119 5.15e+01 1fxoA 293 5.15e+01 1g0rA c.68.1.6 34524 1kv0A 66 5.17e+01 g.3.7.1 91040 1cczA 171 5.19e+01 1cczA b.1.1.1,b.1.1.3 19758,21683 1yua 122 5.20e+01 1yua g.41.3.3,g.41.3.3 45210,45211 2aunA 317 5.23e+01 1pbv 195 5.23e+01 1pbv a.118.3.1 19179 1y80A 210 5.24e+01 2dbsA 90 5.31e+01 1ignA 246 5.34e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1bbpA 173 5.34e+01 1bbpA b.60.1.1 27147 1gkzA 388 5.35e+01 a.29.5.1,d.122.1.4 65268,65269 1iwdA 215 5.35e+01 d.3.1.1 83756 1yarA 233 5.36e+01 2gnrA 145 5.39e+01 1s72S 85 5.39e+01 d.12.1.1 105338 2be1A 339 5.40e+01 1m2kA 249 5.43e+01 c.31.1.5 84754 1wdvA 152 5.44e+01 1qd9A 124 5.45e+01 1qu9A d.79.1.1 39758 2fbaA 492 5.46e+01 1dzfA 215 5.46e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1b77A 228 5.47e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2cr4A 126 5.47e+01 1guuA 52 5.50e+01 a.4.1.3 83332 1i4yA 114 5.51e+01 2mhr a.24.4.1 61738 1hz6A 72 5.52e+01 2ptl d.15.7.1 61429 2fb5A 205 5.54e+01 1suuA 312 5.54e+01 b.68.10.1 99006 1wrjA 156 5.55e+01 2gqrA 237 5.55e+01 1bmtA 246 5.56e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1t8hA 277 5.58e+01 d.194.1.2 106664 1byqA 228 5.59e+01 1yer d.122.1.1 41100 1d2eA 397 5.60e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2aorA 223 5.61e+01 2cx5A 158 5.61e+01 1rypI 222 5.62e+01 d.153.1.4 41877 1v04A 355 5.63e+01 b.68.6.2 100240 2chnA 716 5.71e+01 1on2A 142 5.74e+01 a.4.5.24,a.76.1.1 87103,87104 1sgoA 139 5.78e+01 d.82.3.1 98857 1jnrA 643 5.84e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 2ch8A 201 5.88e+01 1mwwA 128 5.92e+01 d.80.1.4 91483 1m5q1 130 5.94e+01 1bpoA 494 5.94e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1cipA 353 5.95e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2czvC 120 5.95e+01 2sak 121 5.98e+01 2sak d.15.5.1 37711 1zbpA 273 5.99e+01 1wpiA 133 6.05e+01 1yzbA 182 6.06e+01 2fjbA 643 6.08e+01 2f57A 317 6.08e+01 1vjqA 79 6.13e+01 k.43.1.1 100830 1w30A 201 6.13e+01 1t0qC 86 6.23e+01 d.15.12.1 106222 1dzkA 157 6.24e+01 1obpA b.60.1.1 27096 1e19A 314 6.27e+01 1b7bA c.73.1.1 34967 2h03A 291 6.30e+01 1qy6A 274 6.31e+01 b.47.1.1 96574 1tqhA 247 6.33e+01 c.69.1.29 107225 1z57A 339 6.34e+01 2cxcA 144 6.36e+01 1lkkA 105 6.40e+01 1lckA d.93.1.1 40412 2dp5A 332 6.40e+01 1wh8A 111 6.42e+01 1j1hA 144 6.48e+01 b.111.1.1 77056 1x47A 98 6.48e+01 1k4mA 213 6.57e+01 c.26.1.3 77258 1qqgA 264 6.60e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1qzgA 187 6.62e+01 b.40.4.3 96643 1vd2A 89 6.68e+01 d.15.2.2 108517 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