# List of top-scoring protein chains for t2k-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.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 1wkoA 180 3.48e-01 1ykfA 352 4.13e-01 1pedA b.35.1.2,c.2.1.1 24757,29773 1vjqA 79 7.17e-01 k.43.1.1 100830 1ejbA 168 7.39e-01 1rvv1 c.16.1.1 59417 1f0iA 504 8.40e-01 1f0iA d.136.1.2,d.136.1.2 59566,59567 2cu1A 103 8.42e-01 1pjqA 457 8.43e-01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1v0wA 506 9.11e-01 d.136.1.2,d.136.1.2 108220,108221 1xt5A 135 9.66e-01 2cxcA 144 1.26e+00 1yreA 197 1.31e+00 1k4mA 213 1.43e+00 c.26.1.3 77258 1eudA 311 1.58e+00 2scuA c.2.1.8,c.23.4.1 30312,31140 1vb5A 276 1.70e+00 1eucA 311 1.82e+00 2scuA c.2.1.8,c.23.4.1 30311,31139 1fjgP 88 2.09e+00 1emwA d.27.1.1 38444 2ch8A 201 2.14e+00 2ag4A 164 2.30e+00 2ag9A 164 2.39e+00 1mkyA 439 2.42e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1r88A 280 2.43e+00 c.69.1.3 97219 1ehkB 168 2.75e+00 2cuaA b.6.1.2,f.17.2.1 23041,43625 2cuaA 135 2.85e+00 2cuaA b.6.1.2 23039 1ejeA 192 2.88e+00 1ejeA b.45.1.2 25757 1rz1A 161 3.04e+00 b.45.1.2 98124 1pu5A 164 3.04e+00 b.95.1.1 104310 1yal 218 3.17e+00 1cs8A d.3.1.1 37025 1dosA 358 3.31e+00 1dosA c.1.10.2 29175 1y9aA 360 3.57e+00 1v5eA 590 3.64e+00 1b57A 358 3.78e+00 1dosA c.1.10.2 29177 1uhvA 500 4.09e+00 b.71.1.2,c.1.8.3 99402,99403 1kxrA 339 4.19e+00 d.3.1.3 73175 1g13A 162 4.31e+00 1g13A b.95.1.1 60194 1sayA 361 4.32e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 1ww9A 392 4.41e+00 1vq2A 193 4.51e+00 1kgsA 225 4.70e+00 a.4.6.1,c.23.1.1 68596,68597 1tl9A 339 5.08e+00 1qt9A 98 5.25e+00 1awd d.15.4.1 37647 1czpA 98 5.29e+00 1awd d.15.4.1 37645 2a1hA 365 5.57e+00 1nmuB 104 5.71e+00 d.79.3.1 80666 1d3yA 301 5.82e+00 1d3yA e.12.1.1 43252 1w78A 422 5.97e+00 1yfqA 342 6.09e+00 2fliA 220 6.25e+00 1td4A 115 6.34e+00 2coiA 386 6.43e+00 1pedA 351 6.49e+00 1pedA b.35.1.2,c.2.1.1 24753,29769 1sc6A 404 7.04e+00 1hkfA 122 7.10e+00 b.1.1.1 83553 1qouA 181 7.12e+00 1qouA b.17.1.1 23707 1wleA 501 7.24e+00 1lx7A 253 7.26e+00 c.56.2.1 74329 1rxyA 253 7.47e+00 c.56.2.1 98065 1nbwB 117 7.51e+00 c.51.3.2 80396 1vdwA 254 7.74e+00 e.7.1.1 100569 1iyeA 309 7.79e+00 e.17.1.1 83786 1pjbA 361 7.80e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1o8uA 257 8.02e+00 c.14.1.3 81194 1a6q 382 8.05e+00 1a6q a.159.1.1,d.219.1.1 75801,75802 1i1kA 309 8.23e+00 1daaA e.17.1.1 61533 1cbf 285 8.31e+00 1cbf c.90.1.1 35587 1b24A 188 8.53e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1rl6A 177 8.58e+00 1rl6A d.141.1.1,d.141.1.1 41473,41474 1fxjA 331 9.00e+00 1fwyA b.81.1.4,c.68.1.5 28062,34520 1pjcA 361 9.02e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1vhvA 268 9.11e+00 c.90.1.1 100704 1odfA 290 9.24e+00 c.37.1.6 92782 1vpdA 299 9.29e+00 1u4cA 349 9.49e+00 b.69.4.2 107666 1nhcA 336 9.77e+00 b.80.1.3 91879 1emwA 88 1.04e+01 1emwA d.27.1.1 38448 1kt8A 365 1.04e+01 e.17.1.1 77531 1fwyA 331 1.04e+01 1fwyA b.81.1.4,c.68.1.5 28064,34522 2cbf 234 1.04e+01 1cbf c.90.1.1 35588 1zesA 125 1.06e+01 1oi7A 288 1.07e+01 c.2.1.8,c.23.4.1 87049,87050 1hv9A 456 1.11e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1zd9A 188 1.11e+01 1d6zA 727 1.13e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1ktaA 365 1.13e+01 e.17.1.1 77533 1ck9A 104 1.13e+01 1ck9A d.79.3.1 39806 1k3fA 253 1.14e+01 c.56.2.1 68105 1b7bA 310 1.15e+01 1b7bA c.73.1.1 34963 1m2xA 223 1.16e+01 d.157.1.1 84764 1w0mA 226 1.18e+01 c.1.1.1 109027 1ez0A 510 1.23e+01 1eyyA c.82.1.1 35385 1g2iA 166 1.24e+01 1g2iA c.23.16.2 31438 1hv8A 367 1.26e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1fxiA 96 1.28e+01 1awd d.15.4.1 37664 1o5zA 442 1.29e+01 c.59.1.2,c.72.2.2 92530,92531 2tbd 134 1.31e+01 2tbd d.89.1.1 40241 2g8jA 339 1.32e+01 1tig 94 1.32e+01 1tig d.68.1.1 39566 1bcsB 160 1.32e+01 1whtB 1jqbA 351 1.33e+01 b.35.1.2,c.2.1.1 77151,77152 1a3gA 308 1.43e+01 1daaA e.17.1.1 43286 1ekfA 365 1.43e+01 1ekfA e.17.1.1 59445 1vpjA 192 1.48e+01 1kevA 351 1.50e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1e3mA 800 1.51e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1krhA 338 1.54e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1booA 323 1.55e+01 1booA c.66.1.11 34248 1e9rA 437 1.57e+01 c.37.1.11 64827 1l5zA 155 1.58e+01 c.23.1.1 77722 1tluA 130 1.62e+01 d.156.1.2 107139 1klo 162 1.62e+01 1klo g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 1zm0A 114 1.64e+01 1lylA 504 1.66e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1a73A 163 1.66e+01 1a73A d.4.1.3 37145 2cwzA 141 1.67e+01 1wd5A 208 1.68e+01 1gr0A 367 1.68e+01 c.2.1.3,d.81.1.3 70379,70380 1f2vA 219 1.73e+01 1f2vA c.23.17.1 59627 1b34A 119 1.77e+01 1d3bA b.38.1.1 24796 1ddgA 374 1.77e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1xx0A 127 1.78e+01 1y0yA 353 1.78e+01 1a48 306 1.80e+01 1a48 d.143.1.1 41590 1x6oA 174 1.80e+01 b.34.5.2,b.40.4.5 109493,109494 1whsB 153 1.80e+01 1whtB 1qkkA 155 1.81e+01 1dbwA c.23.1.1 31104 2cnqA 306 1.83e+01 1kzhA 555 1.88e+01 c.89.1.1 73361 1vgjA 184 1.88e+01 1nt4A 391 1.88e+01 c.60.1.2 92102 1t9bA 677 1.89e+01 1xm8A 254 1.90e+01 1w1hA 151 1.96e+01 1o6aA 96 1.97e+01 b.139.1.1 92562 2fiqA 420 1.98e+01 1oaoA 674 1.98e+01 e.26.1.2 86744 1zid 268 2.01e+01 1eny c.2.1.2 29911 1obdA 306 2.04e+01 d.143.1.1 86767 1tiiD 99 2.05e+01 1tiiD b.40.2.1 24965 1whtB 153 2.06e+01 1whtB 1p57A 114 2.06e+01 d.170.1.2 94125 1poxA 585 2.10e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1dts 221 2.14e+01 1byi c.37.1.10 32200 1m2dA 110 2.16e+01 c.47.1.11 78476 1xfoA 357 2.21e+01 1nh1A 330 2.21e+01 e.45.1.1 91871 1rfkA 98 2.23e+01 2g0cA 76 2.25e+01 1euvB 86 2.26e+01 1a5r d.15.1.1 37598 1ve2A 235 2.32e+01 1xwfA 431 2.33e+01 3ullA 132 2.37e+01 3ullA b.40.4.3 25282 1eyyA 510 2.39e+01 1eyyA c.82.1.1 35389 1q1aA 289 2.41e+01 c.31.1.5 95561 1pytC 253 2.43e+01 5ptp b.47.1.2 26233 1oe4A 247 2.45e+01 c.18.1.3 86895 1q0uA 219 2.45e+01 c.37.1.19 95512 1gsa 316 2.46e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 2bzlA 325 2.49e+01 1id1A 153 2.50e+01 1id1A c.2.1.9 62286 1pv9A 348 2.50e+01 c.55.2.1,d.127.1.1 95157,95158 1bh5A 183 2.53e+01 1qipA d.32.1.1 38476 1ak2 233 2.54e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1h7zA 194 2.55e+01 1qhvA b.21.1.1 60733 1zkeA 83 2.57e+01 1d4fA 431 2.66e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1j3bA 529 2.66e+01 c.91.1.1,c.109.1.1 77071,77072 1evxA 162 2.67e+01 1a73A d.4.1.3 37149 2c07A 285 2.67e+01 1ta3A 274 2.69e+01 c.1.8.5 106731 1o66A 275 2.70e+01 c.1.12.8 92547 1ip9A 85 2.70e+01 1ip9A d.15.2.2 62638 1spuB 727 2.73e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1aky 221 2.75e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1om0A 274 2.75e+01 c.1.8.5 87058 1x1gA 129 2.78e+01 1offA 97 2.82e+01 d.15.4.1 86947 1jmmA 377 2.83e+01 b.30.6.1 71749 1glv 303 2.88e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 2ew8A 249 2.88e+01 1em2A 229 2.89e+01 1em2A d.129.3.2 41321 1qupA 222 2.89e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1s62A 106 2.90e+01 1d3bB 91 2.90e+01 1d3bB b.38.1.1 24804 2aq8A 269 2.95e+01 1tbd 134 2.98e+01 2tbd d.89.1.1 40240 1tf1A 198 3.00e+01 d.110.2.2 106826 1rpxA 230 3.02e+01 1rpxA c.1.2.2 28536 1qb5D 99 3.03e+01 b.40.2.1 88357 9apiA 347 3.04e+01 1ovaA e.1.1.1 42630 2as9A 210 3.05e+01 1ukuA 102 3.06e+01 d.58.5.2 99533 1qlpA 394 3.07e+01 1ovaA e.1.1.1 42628 1aisB 200 3.08e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1jscA 630 3.09e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1ck2A 104 3.10e+01 1ck9A d.79.3.1 39809 1srrA 124 3.10e+01 1dz3A c.23.1.1 31110 2ez9A 603 3.14e+01 1i1hA 219 3.19e+01 1f2vA c.23.17.1 61530 2c78A 405 3.19e+01 1eft 405 3.23e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 2etgA 296 3.25e+01 1wf3A 301 3.28e+01 1xppA 115 3.30e+01 1zl0A 311 3.30e+01 1v9fA 325 3.31e+01 d.265.1.3 108448 1frd 98 3.34e+01 1awd d.15.4.1 37648 1dbwA 126 3.35e+01 1dbwA c.23.1.1 31095 2g9iA 249 3.36e+01 1g61A 228 3.39e+01 1g61A d.126.1.1 41126 1i24A 404 3.41e+01 c.2.1.2 83663 1oacA 727 3.42e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1atu 374 3.45e+01 1ovaA e.1.1.1 42636 1pk6C 129 3.50e+01 b.22.1.1 94803 1ej8A 140 3.50e+01 1qupA b.1.8.1 22300 1ns5A 155 3.59e+01 c.116.1.3 80705 1gq6A 313 3.61e+01 c.42.1.1 70341 1iuhA 198 3.64e+01 d.61.1.2 83711 1mhxA 65 3.70e+01 d.15.7.1 79134 1vm7A 311 3.72e+01 c.72.1.1 108884 1efcA 393 3.72e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1yovA 537 3.74e+01 1iqsA 88 3.76e+01 d.214.1.1 71278 1veaA 148 3.80e+01 d.275.1.1 108529 3stdA 165 3.84e+01 3stdA d.17.4.1 38073 1fonA 240 3.94e+01 5ptp b.47.1.2 26231 1lxa 262 4.04e+01 1lxa b.81.1.1 28052 2fr2A 172 4.10e+01 2aq9A 262 4.11e+01 1oj7A 408 4.16e+01 e.22.1.2 103971 1kid 203 4.22e+01 1derA c.8.5.1 30771 1v88A 130 4.23e+01 b.55.1.1 108423 1cjsA 219 4.25e+01 1cjsA e.24.1.1 43354 1qrrA 394 4.25e+01 1qrrA c.2.1.2 29824 1kafA 108 4.28e+01 d.199.1.1 68372 1psdA 409 4.36e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1zrsA 317 4.38e+01 2aumA 317 4.39e+01 1g2oA 268 4.39e+01 1b8oA c.56.2.1 60228 1efuA 385 4.40e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1nkoA 132 4.43e+01 b.1.1.1 85829 1pe0A 197 4.44e+01 c.23.16.2 88045 1eny 268 4.44e+01 1eny c.2.1.2 29910 1hv2A 99 4.48e+01 d.42.1.1 61287 1jzuA 157 4.49e+01 b.60.1.1 84271 2b0vA 153 4.50e+01 1k3sA 113 4.51e+01 d.198.1.1 68120 1sqrA 95 4.55e+01 1przA 252 4.56e+01 d.265.1.3 95064 1d3uB 201 4.56e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1f37A 110 4.57e+01 1f37A c.47.1.11 33088 1o6dA 163 4.58e+01 c.116.1.3 92567 2aunA 317 4.60e+01 1r6vA 671 4.62e+01 1p5fA 189 4.64e+01 c.23.16.2 94142 1szoA 257 4.67e+01 c.14.1.3 106164 1oltA 457 4.67e+01 c.1.28.2 93334 2dfkA 402 4.67e+01 1vq0A 302 4.72e+01 1n08A 163 4.72e+01 b.43.5.1 79730 1x54A 434 4.72e+01 1op3H 225 4.80e+01 b.1.1.1,b.1.1.2 87208,87209 1ob8A 135 4.83e+01 1fx3A 169 4.84e+01 1fx3B d.33.1.1 38524 1umkA 275 4.85e+01 1nksA 194 4.91e+01 1nksA c.37.1.1 31886 1bg6 359 4.93e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1e3pA 757 4.94e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1e12A 253 4.96e+01 1c3wA f.13.1.1 43428 1h3fA 432 4.98e+01 c.26.1.1,d.66.1.4 76631,76632 1vr7A 142 5.00e+01 1uv7A 110 5.01e+01 d.67.4.1 100040 1fqtA 112 5.04e+01 1fqtA b.33.1.1 24441 1dckA 126 5.04e+01 1dbwA c.23.1.1 31097 1fx3B 169 5.08e+01 1fx3B d.33.1.1 38525 1othA 321 5.21e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1x42A 232 5.32e+01 1vkyA 347 5.42e+01 e.53.1.1 108696 1tzaA 134 5.52e+01 b.1.23.1 107468 1so9A 164 5.55e+01 b.146.1.1 105842 1t6nA 220 5.55e+01 c.37.1.19 106576 2fa1A 160 5.58e+01 1u0tA 307 5.59e+01 e.52.1.1 107567 1f3aA 222 5.59e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1hhsA 664 5.62e+01 1hi0P e.8.1.6 61045 1lxjA 104 5.63e+01 d.58.48.1 84736 2glfA 450 5.64e+01 1vclA 432 5.67e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1wjgA 137 5.69e+01 2std 172 5.69e+01 3stdA d.17.4.1 38085 1h75A 81 5.70e+01 1h75A c.47.1.1 60716 1jpnA 296 5.70e+01 a.24.13.1,c.37.1.10 67039,67040 1qfxA 460 5.73e+01 1qfxA c.60.1.2 33994 1j2zA 270 5.75e+01 b.81.1.1 90805 1g1xC 88 5.77e+01 1fjfR a.4.8.1 16249 1ztxE 108 5.77e+01 1kl9A 182 5.78e+01 b.40.4.5 72681 1f1sA 814 5.78e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1u9cA 224 5.82e+01 1amj 754 5.86e+01 1amj c.8.2.1,c.83.1.1 30725,35401 1uarA 285 5.89e+01 c.46.1.2,c.46.1.2 107762,107763 1jiwI 106 5.89e+01 1smpI b.61.2.1 63078 1u8zA 168 5.93e+01 1gr5A 547 5.93e+01 i.16.1.1 65478 1cf1A 404 5.94e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1nqeA 594 5.97e+01 f.4.3.3 86027 1ii6A 368 6.02e+01 1bg2 c.37.1.9 62413 1ydgA 211 6.02e+01 2ge7A 108 6.03e+01 1pueE 89 6.03e+01 1awcA a.4.5.21 16165 1pfsA 78 6.08e+01 1pfsA b.40.4.7 25391 1jkmB 361 6.10e+01 1jkmA c.69.1.2 34634 1wmbA 260 6.13e+01 1oy1A 228 6.20e+01 c.23.16.2 87548 1m0qA 433 6.21e+01 c.67.1.4 78350 1wb9A 800 6.22e+01 1cc1S 283 6.22e+01 2frvA e.19.1.1 43313 1m2aA 110 6.23e+01 c.47.1.11 78472 1mjfA 281 6.23e+01 c.66.1.17 79198 1ov3A 138 6.23e+01 b.34.2.1,b.34.2.1 87451,87452 1t7lA 766 6.25e+01 1k5cA 335 6.28e+01 b.80.1.3 72076 1j0dA 341 6.28e+01 c.79.1.1 83902 2fox 138 6.31e+01 5nul c.23.5.1 31197 1kewA 361 6.34e+01 c.2.1.2 68544 1i2aA 219 6.40e+01 e.24.1.1 90660 1rie 129 6.41e+01 1rie b.33.1.1 24427 1ls1A 295 6.43e+01 a.24.13.1,c.37.1.10 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