# List of top-scoring protein chains for t04-100-30-bys-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 1vjkA 98 1.11e-04 d.15.3.1 108631 1rwsA 77 1.63e-03 d.15.3.2 97991 1oqqA 106 3.18e-03 d.15.4.1 93422 1frrA 95 1.74e-02 1awd d.15.4.1 37674 1xlqA 106 2.14e-02 1fm0D 81 2.93e-02 1fmaD d.15.3.1 37642 1uwmA 106 4.57e-02 1e9mA 106 4.67e-02 1ayfA d.15.4.1 59397 1jl0A 334 7.65e-02 1jenA d.156.1.1 63155 1jenA 267 7.73e-02 1jenA 1ryjA 70 1.03e-01 d.15.3.2 98104 1qorA 327 2.63e-01 1qorA b.35.1.2,c.2.1.1 24766,29782 2bb6A 414 2.66e-01 1frd 98 3.91e-01 1awd d.15.4.1 37648 2f4pA 147 4.27e-01 1ra6A 461 4.40e-01 e.8.1.4 104879 2cu3A 64 4.56e-01 1k07A 263 4.80e-01 d.157.1.1 77218 1i7hA 111 5.16e-01 d.15.4.1 71122 1zud2 66 6.33e-01 1l5pA 93 6.53e-01 d.15.4.1 73598 1zpuA 534 8.67e-01 1rdr 461 8.72e-01 1rdr e.8.1.4 43116 1zu0A 529 8.96e-01 1doi 128 9.34e-01 1awd d.15.4.1 37676 1awd 94 1.06e+00 1awd d.15.4.1 37673 1dmhA 311 1.14e+00 1dmhA b.3.6.1 22633 1rfkA 98 1.16e+00 2bwfA 77 1.28e+00 1czpA 98 1.44e+00 1awd d.15.4.1 37645 1r5lA 262 1.53e+00 a.5.3.1,c.13.1.1 97099,97100 1woqA 267 1.67e+00 c.55.1.10,c.55.1.10 109462,109463 2al3A 90 1.97e+00 1f1uA 323 2.05e+00 d.32.1.3,d.32.1.3 83200,83201 1offA 97 2.30e+00 d.15.4.1 86947 1o5oA 221 2.42e+00 c.61.1.1 92509 2g1lA 104 2.59e+00 1siqA 392 2.61e+00 a.29.3.1,e.6.1.1 105585,105586 1l2hA 153 2.92e+00 b.42.1.2 77655 1r3eA 309 3.15e+00 b.122.1.1,d.265.1.2 96907,96908 1nw1A 429 3.21e+00 d.144.1.8 86286 2bpsA 81 3.37e+00 1omzA 293 3.41e+00 c.68.1.15 87093 1pvc3 238 3.51e+00 1aym3 1f1xA 322 3.53e+00 d.32.1.3,d.32.1.3 83208,83209 1vr6A 350 4.31e+00 1xdyA 298 4.65e+00 1uasA 362 4.66e+00 b.71.1.1,c.1.8.1 88388,88389 1wwkA 307 4.66e+00 1pvmA 184 4.88e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1a70 97 5.25e+00 1awd d.15.4.1 37678 1gpr 162 5.48e+00 1gpr b.84.3.1 28267 1cxyA 90 6.24e+00 1cyo d.120.1.1 41085 1wruA 379 6.42e+00 2azwA 148 7.11e+00 1s0uA 408 7.19e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1vf7A 369 7.85e+00 f.46.1.1 108557 1xc3A 302 8.12e+00 1wgrA 100 8.44e+00 1ubi 76 8.91e+00 1ubi d.15.1.1 37584 1owfB 94 9.23e+00 a.55.1.1 87488 2fcr 173 9.74e+00 1rcf c.23.5.1 31151 1ayfA 105 1.00e+01 1ayfA d.15.4.1 37684 1vp4A 425 1.01e+01 1yj1A 76 1.04e+01 1q2wA 308 1.14e+01 b.47.1.4 88355 2a4hA 126 1.15e+01 1agjA 242 1.19e+01 1agjA b.47.1.1 25827 1kqfC 217 1.19e+01 f.21.1.1 72874 2gaxA 135 1.20e+01 1nbfD 76 1.21e+01 d.15.1.1 80390 2i1b 153 1.27e+01 2i1b b.42.1.2 25538 1wm3A 72 1.29e+01 1ykdA 398 1.32e+01 1tqxA 227 1.35e+01 1vybA 238 1.37e+01 d.151.1.1 108897 1ku0A 388 1.39e+01 c.69.1.18 72994 1t6aA 126 1.39e+01 d.129.8.1 106555 1l7aA 318 1.39e+01 c.69.1.25 77772 1knmA 130 1.43e+01 b.42.2.1 72781 1twfK 120 1.44e+01 1qtnA 164 1.44e+01 1pauA c.17.1.1 30999 2bh8A 101 1.44e+01 3grs 478 1.45e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1wstA 417 1.45e+01 1bpyA 335 1.53e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 2aj2A 208 1.55e+01 1euvB 86 1.56e+01 1a5r d.15.1.1 37598 1qmvA 197 1.56e+01 1qq2A c.47.1.10 33066 1uqtA 482 1.56e+01 c.87.1.6 99794 1sfe 180 1.56e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1i50K 120 1.58e+01 d.74.3.2 61765 2bt6A 108 1.64e+01 1l7yA 94 1.65e+01 d.15.1.6 73676 2et1A 201 1.69e+01 1uwwA 191 1.69e+01 b.18.1.23 108079 2azeB 106 1.73e+01 2a5kA 307 1.76e+01 1q5dA 419 1.77e+01 a.104.1.1 95891 1ktbA 405 1.77e+01 b.71.1.1,c.1.8.1 72960,72961 2h1tA 188 1.83e+01 2apoA 357 1.86e+01 1dl5A 317 1.88e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2g8lA 299 1.91e+01 1f4qA 165 1.92e+01 1alvA a.39.1.8 17360 2f96A 224 1.95e+01 2bodX 286 1.96e+01 2d42A 249 1.98e+01 1pgs 314 1.98e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1ogwA 76 1.99e+01 d.15.1.1 87001 2cfeA 162 2.01e+01 1h9sA 140 2.04e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1k94A 165 2.04e+01 a.39.1.8 68333 1zvtA 256 2.18e+01 1tmxA 293 2.22e+01 1jb3A 131 2.29e+01 1jc7A b.40.3.2 62833 1pg4A 652 2.35e+01 e.23.1.1 88067 1q2lA 939 2.42e+01 1vhzA 198 2.46e+01 d.113.1.1 100718 2sns 149 2.52e+01 1snc b.40.1.1 24860 1ejbA 168 2.53e+01 1rvv1 c.16.1.1 59417 2as0A 396 2.53e+01 1vknA 351 2.59e+01 c.2.1.3,d.81.1.1 108676,108677 2gptA 523 2.62e+01 2fug1 438 2.62e+01 1ubeA 349 2.64e+01 c.37.1.11,d.48.1.1 88412,88413 2fmpA 335 2.68e+01 1snzA 344 2.69e+01 b.30.5.4 98930 1b9rA 105 2.70e+01 1ayfA d.15.4.1 37683 1befA 181 2.71e+01 1befA b.47.1.3 26419 1m93B 245 2.75e+01 2c36A 285 2.79e+01 1zn8A 180 2.80e+01 2gupA 292 2.83e+01 1pl8A 356 2.83e+01 b.35.1.2,c.2.1.1 94878,94879 2fexA 188 2.84e+01 1vioA 243 2.86e+01 d.265.1.3,d.66.1.5 100762,100763 1p4oA 322 2.86e+01 d.144.1.7 87775 1ad2 228 2.87e+01 1ad2 e.24.1.1 43353 1fi2A 201 2.89e+01 1fi2A b.82.1.2 59845 1htrP 43 2.91e+01 1htrP b.50.1.2 26852 2amdA 311 2.93e+01 1ypyA 184 2.93e+01 1v4aA 440 2.94e+01 a.24.16.4,d.218.1.9 108350,108351 2b0vA 153 3.08e+01 1e6eB 128 3.10e+01 1ayfA d.15.4.1 59300 1gsmA 210 3.11e+01 b.1.1.4,b.1.1.4 65535,65536 1b9mA 265 3.12e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1cf2O 337 3.23e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1tv9A 335 3.26e+01 1vmiA 355 3.26e+01 2fcfA 103 3.32e+01 1o54A 277 3.33e+01 c.66.1.13 92482 1k8wA 327 3.37e+01 b.122.1.1,d.265.1.2 83094,90388 2a4vA 159 3.39e+01 1wjnA 97 3.47e+01 1xkpA 246 3.49e+01 1yqtA 538 3.56e+01 1v9sA 208 3.58e+01 1wmzA 140 3.58e+01 d.169.1.1 109422 1p3qQ 54 3.63e+01 a.5.2.4 87748 1irsA 112 3.66e+01 1qqgA b.55.1.2 26991 1yzhA 214 3.67e+01 1ub0A 258 3.70e+01 c.72.1.2 88394 1txnA 328 3.71e+01 2es7A 142 3.71e+01 1gcqC 70 3.74e+01 1gcpA b.34.2.1 60436 1nh9A 87 3.75e+01 d.68.6.1 91878 1ktgA 138 3.75e+01 d.113.1.1 72972 1c1yB 77 3.79e+01 1c1yB d.15.1.5 37618 1h8eA 510 3.79e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1ftkA 279 3.83e+01 1gr2A c.94.1.1 35819 4tsvA 150 3.85e+01 2tnfA b.22.1.1 23860 1ir3A 306 3.85e+01 1fmk d.144.1.7 41702 1v8fA 276 3.90e+01 c.26.1.4 100503 1o4sA 389 3.94e+01 c.67.1.1 86620 1gxuA 91 3.97e+01 d.58.10.1 76378 1kk1A 410 3.98e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1n3jA 119 4.02e+01 b.85.7.2 79963 1mqiA 263 4.05e+01 c.94.1.1 91398 1hdmA 201 4.07e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1cnzA 363 4.10e+01 1cnzA c.77.1.1 35061 1zyeA 220 4.10e+01 1ey4A 149 4.10e+01 1snc b.40.1.1 24815 1n83A 270 4.11e+01 a.123.1.1 80276 2fv1A 377 4.19e+01 2fomB 185 4.26e+01 1eokA 290 4.28e+01 1eokA c.1.8.5 28991 1txqA 93 4.28e+01 1qrvA 73 4.29e+01 1cktA a.21.1.1 16425 1ofuA 320 4.29e+01 c.32.1.1,d.79.2.1 86972,86973 1yfbA 59 4.30e+01 2d7nA 93 4.31e+01 1otgA 125 4.32e+01 1otgA d.80.1.2 39831 1fvrA 327 4.32e+01 d.144.1.7 60047 1tk1A 260 4.39e+01 d.248.1.1 107066 1vd5A 377 4.41e+01 a.102.1.7 108518 1uj8A 77 4.45e+01 1oi2A 366 4.73e+01 c.119.1.2 103802 1dg6A 191 4.74e+01 1d4vB b.22.1.1 23883 1dljA 402 4.74e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1aohA 147 4.75e+01 1aohA b.2.2.2 22401 1f6dA 376 4.77e+01 1f6dA c.87.1.3 35467 1o17A 345 4.81e+01 a.46.2.1,c.27.1.1 80765,80766 1xe1A 116 4.87e+01 b.43.3.1 109571 1lxiA 139 4.88e+01 g.17.1.2 84735 2akoA 251 4.89e+01 1lfdA 87 5.01e+01 1lfdA d.15.1.5 37622 1g0sA 209 5.04e+01 1g0sA d.113.1.1 60187 1x3zB 72 5.05e+01 2h2bA 107 5.05e+01 1wkaA 147 5.05e+01 2au3A 407 5.05e+01 1vlaA 150 5.11e+01 d.227.1.2 108735 2gcuA 245 5.14e+01 1e79A 510 5.15e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1in0A 163 5.16e+01 d.58.49.1,d.58.49.1 83694,83695 2c5lC 117 5.29e+01 1e2wA 251 5.29e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1d02A 202 5.30e+01 1d02A c.52.1.8 33313 1egpA 45 5.48e+01 1egpA d.40.1.1 38561 1tp6A 128 5.52e+01 d.17.4.12 107184 1zn6A 227 5.52e+01 1vq2A 193 5.63e+01 1onrA 316 5.66e+01 1onrA c.1.10.1 29169 1to2I 64 5.67e+01 1o50A 157 5.73e+01 d.37.1.1,d.37.1.1 92478,92479 1j3mA 129 5.81e+01 d.129.7.1 103836 1i2oA 316 5.82e+01 1onrA c.1.10.1 61574 1bc8C 93 5.85e+01 1awcA a.4.5.21 16168 1iv8A 720 5.89e+01 b.71.1.1,c.1.8.1 76842,76843 1fmtA 314 5.94e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2ck3A 510 6.07e+01 2c9lY 63 6.10e+01 1lktA 104 6.27e+01 1lktA b.90.1.1 28398 1otrA 49 6.27e+01 a.5.2.4 87413 1tc6A 236 6.32e+01 d.122.1.1 106756 1sjyA 159 6.39e+01 d.113.1.1 98900 1fa8A 135 6.45e+01 1qipA d.32.1.1 38486 1ypcI 64 6.53e+01 2sniI d.40.1.1 38570 1ylxA 103 6.54e+01 1nhs 447 6.57e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1wehA 171 6.58e+01 1ep3B 262 6.67e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1z3qA 200 6.71e+01 2fqmA 75 6.95e+01 1v76A 96 6.95e+01 1qlaC 256 6.98e+01 1qlaC f.21.2.1 43722 1uliA 460 6.98e+01 b.33.1.2,d.129.3.3 107921,107922 1tml 286 7.00e+01 1tml c.6.1.1 30656 1jsdA 319 7.01e+01 b.19.1.2 63258 2ab0A 205 7.09e+01 1xt8A 292 7.19e+01 1lw6I 64 7.20e+01 d.40.1.1 74294 1se9A 126 7.26e+01 d.15.1.1 98821 1wmmA 145 7.53e+01 1vkyA 347 7.57e+01 e.53.1.1 108696 6cel 434 7.63e+01 1celA b.29.1.10 24279 2b3nA 159 7.65e+01 1ghhA 81 7.67e+01 1ghhA d.57.1.1 38940 1bbhA 131 7.67e+01 1bbhA a.24.3.2 16546 2ah5A 210 7.72e+01 1t5hX 504 7.73e+01 e.23.1.1 106449 1cc8A 73 7.74e+01 1cc8A d.58.17.1 39343 2a6hD 1524 7.84e+01 1rl0A 255 7.88e+01 1ucsA 64 8.06e+01 b.85.1.1 88466 1pk1B 89 8.07e+01 1jvwA 167 8.10e+01 d.26.1.1 71907 1oruA 195 8.11e+01 b.58.1.2 93464 1x1mA 107 8.18e+01 2evbA 74 8.24e+01 1u09A 476 8.35e+01 e.8.1.4 107545 1el6A 219 8.37e+01 1el6B d.182.1.1 42606 1zboA 210 8.37e+01 1e3jA 352 8.40e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1ixmA 192 8.45e+01 1ixmA d.123.1.1 41114 1f0cA 305 8.48e+01 1c8oA e.1.1.1 42676 1k8kC 372 8.52e+01 b.69.4.1 68308 1ws8A 109 8.53e+01 1pbgA 468 8.54e+01 1e70M c.1.8.4 28946 1sz6B 263 8.57e+01 2reb 352 8.64e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1u0tA 307 8.67e+01 e.52.1.1 107567 1tfuA 157 8.76e+01 c.26.1.3 106859 1jae 471 8.80e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1har 216 8.91e+01 1rthA e.8.1.2 43025 1pcxA 810 8.94e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 2gimA 106 8.97e+01 1yeyA 444 8.97e+01