# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1yr0A 175 4.40e-21 2ge3A 170 2.17e-20 1yvoA 172 3.38e-20 2bl1A 172 3.54e-20 1vhsA 175 1.77e-19 d.108.1.1 100698 2ae6A 166 1.65e-18 1tiqA 180 1.69e-18 d.108.1.1 107010 2fe7A 166 1.69e-17 2beiA 170 8.90e-17 2cy2A 174 9.81e-17 1nslA 184 1.10e-16 d.108.1.1 86137 1z4eA 153 9.99e-16 1wwzA 159 1.92e-15 1u6mA 199 4.30e-15 2b5gA 171 7.05e-15 1s7kA 182 1.43e-14 1s3zA 165 5.76e-14 d.108.1.1 105250 1gheA 177 8.81e-14 d.108.1.1 76222 2fckA 181 1.08e-13 1yreA 197 1.15e-13 2fl4A 149 1.31e-13 1qsoA 149 3.56e-13 1qsmA d.108.1.1 40812 1on0A 158 4.08e-13 d.108.1.1 87095 1qsmA 152 5.42e-13 1qsmA d.108.1.1 40808 1y9kA 157 6.58e-13 1mk4A 157 3.56e-12 d.108.1.1 84979 1i1dA 161 3.69e-12 1i21A d.108.1.1 61526 1i12A 160 4.03e-12 1i21A d.108.1.1 61515 1vkcA 158 6.72e-12 1cjwA 166 4.27e-11 1cjwA d.108.1.1 40818 1yvkA 163 4.30e-11 1n71A 180 4.97e-11 d.108.1.1 85370 1b87A 181 5.92e-11 1b87A d.108.1.1 40797 2a4nA 182 7.28e-11 1qstA 160 3.30e-10 1yghA d.108.1.1 40804 2c27A 315 3.48e-10 1yx0A 159 4.32e-10 1p0hA 318 7.56e-10 d.108.1.1 93866 2bswA 146 8.08e-10 1q2yA 140 8.45e-10 d.108.1.1 95655 2fsrA 195 9.51e-10 1y9wA 140 9.56e-10 1z4rA 168 1.08e-09 2atrA 138 2.76e-09 2g3aA 152 2.98e-09 1y7rA 133 5.13e-09 1yghA 164 1.93e-08 1yghA d.108.1.1 40802 2ganA 190 3.11e-08 1bo4A 168 3.62e-08 1bo4A d.108.1.1 40798 1sqhA 312 4.67e-08 d.108.1.5 98966 1m4iA 181 1.35e-07 d.108.1.1 74457 1yk3A 210 2.49e-07 2aj6A 159 2.60e-07 1xebA 150 1.03e-06 2d4pA 141 4.15e-05 1bob 320 1.45e-04 1bob d.108.1.1 40816 1yleA 342 5.03e-04 1fy7A 278 9.01e-03 1fy7A d.108.1.1 40817 1iicA 422 1.19e-02 1nmtA d.108.1.2,d.108.1.2 62422,62423 1kzfA 230 1.44e-02 d.108.1.3 73354 1xmtA 103 2.97e-02 2givA 295 4.29e-02 1ne9A 335 1.63e-01 d.108.1.4,d.108.1.4 91839,91840 1y0bA 197 2.90e-01 1zejA 293 5.19e-01 1svjA 156 7.35e-01 d.220.1.1 106049 1y81A 138 7.77e-01 1o50A 157 8.72e-01 d.37.1.1,d.37.1.1 92478,92479 1ro5A 201 1.33e+00 d.108.1.3 105023 1shdA 107 1.40e+00 1fmk d.93.1.1 40440 1f1uA 323 1.59e+00 d.32.1.3,d.32.1.3 83200,83201 1han 297 1.69e+00 1han d.32.1.3,d.32.1.3 38506,38507 1rfmA 344 1.73e+00 c.122.1.1 97385 1lkdA 297 1.78e+00 d.32.1.3,d.32.1.3 78059,78060 1afwA 393 1.86e+00 1afwA c.95.1.1,c.95.1.1 35900,35901 1wxdA 263 2.21e+00 2d5cA 263 2.23e+00 1pixA 587 2.42e+00 c.14.1.4 94708 1nkiA 135 2.48e+00 d.32.1.2 91941 1lqpA 135 2.51e+00 d.32.1.2 78151 1lfwA 470 2.52e+00 c.56.5.4,d.58.19.1 77942,77943 1tuoA 464 2.55e+00 2cy0A 263 2.55e+00 1oltA 457 2.88e+00 c.1.28.2 93334 1kllA 130 2.97e+00 d.32.1.2 72720 1pbjA 125 2.98e+00 d.37.1.1,d.37.1.1 94414,94415 1qflA 389 3.01e+00 1afwA c.95.1.1,c.95.1.1 35908,35909 2f46A 156 3.21e+00 1v2xA 194 3.25e+00 c.116.1.1 100274 2arhA 203 3.81e+00 1j08A 226 3.90e+00 c.47.1.2,c.47.1.2 83855,83856 1m3kA 392 3.91e+00 c.95.1.1,c.95.1.1 78565,78566 1f1xA 322 3.92e+00 d.32.1.3,d.32.1.3 83208,83209 1m4tA 392 3.93e+00 c.95.1.1,c.95.1.1 78617,78618 1fjgK 129 3.96e+00 1fjfK c.55.4.1 33733 1v5vA 401 4.06e+00 1xbfA 140 4.34e+00 d.273.1.1 109538 1edzA 320 4.73e+00 1ee9A c.2.1.7,c.58.1.2 30287,33935 1g2qA 187 4.96e+00 c.61.1.1 65117 1f9mA 112 5.19e+00 1erv c.47.1.1 32736 1uyrA 737 5.24e+00 c.14.1.4,c.14.1.4 100188,100189 1w2xA 758 5.38e+00 c.14.1.4,c.14.1.4 109134,109135 1faaA 124 5.43e+00 1erv c.47.1.1 32738 1l3kA 196 5.50e+00 d.58.7.1,d.58.7.1 73539,73540 1qysA 106 5.73e+00 k.41.1.1 96603 1o6aA 96 5.97e+00 b.139.1.1 92562 1zybA 232 6.00e+00 1zh5A 195 6.10e+00 2ew2A 316 6.23e+00 1pvmA 184 6.26e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1h75A 81 6.28e+00 1h75A c.47.1.1 60716 1riqA 465 6.31e+00 a.203.1.1,d.104.1.1 97516,97517 1d5tA 433 6.59e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1p0kA 349 6.78e+00 c.1.4.1 87648 2f57A 317 7.07e+00 1lrzA 426 7.11e+00 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1v9nA 360 7.16e+00 1pot 325 7.53e+00 1pot c.94.1.1 35807 1vl8A 267 7.87e+00 c.2.1.2 108733 2awpA 198 8.11e+00 1zzmA 259 8.14e+00 1ss4A 153 8.62e+00 d.32.1.6 105976 1o5oA 221 8.94e+00 c.61.1.1 92509 1iznB 277 8.95e+00 e.43.1.2 83848 1tljA 213 9.00e+00 d.282.1.1 107126 1xnzA 264 9.45e+00 1shbA 104 9.78e+00 1fmk d.93.1.1 40425 1ha1 184 9.85e+00 1ha1 d.58.7.1,d.58.7.1 39147,39148 1r9dA 787 1.01e+01 c.7.1.1 104865 2pfkA 320 1.02e+01 3pfk c.89.1.1 35577 1ojrA 274 1.03e+01 c.74.1.1 93147 1c24A 263 1.03e+01 1c24A d.127.1.1 41148 1mxgA 435 1.05e+01 b.71.1.1,c.1.8.1 85193,85194 1pfkA 320 1.05e+01 3pfk c.89.1.1 35575 1ztuA 341 1.06e+01 1s4iA 175 1.10e+01 1kyfA 247 1.12e+01 b.1.10.1,d.105.1.1 73220,73221 1qtsA 247 1.14e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1xtlA 175 1.15e+01 1g8yA 279 1.19e+01 1g8yA c.37.1.11 32302 2gtqA 867 1.21e+01 1y1uA 585 1.24e+01 1kw3B 292 1.24e+01 d.32.1.3,d.32.1.3 77549,77550 1gsa 316 1.30e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1xtmA 175 1.33e+01 2db1A 118 1.34e+01 2bhmA 164 1.38e+01 2btfA 375 1.38e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1ne6A 283 1.42e+01 b.82.3.2,b.82.3.2 91831,91832 4pfk 319 1.47e+01 3pfk c.89.1.1 35582 2fyxA 143 1.50e+01 1zmaA 118 1.59e+01 1xsnA 335 1.61e+01 1h5rA 293 1.61e+01 c.68.1.6 65623 1nxuA 333 1.62e+01 c.122.1.1 86389 1faeA 629 1.63e+01 1fce a.102.1.2 18837 1vmaA 306 1.70e+01 a.24.13.1,c.37.1.10 108887,108888 1u0mA 382 1.71e+01 c.95.1.2,c.95.1.2 107557,107558 1g9gA 629 1.71e+01 a.102.1.2 83279 1zxxA 319 1.75e+01 1q7zA 566 1.79e+01 c.1.21.2,c.1.26.1 96090,96091 1dik 874 1.80e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2ggcA 263 1.85e+01 1kpf 126 1.89e+01 1kpf d.13.1.1 37507 1a8l 226 1.89e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1to6A 371 1.92e+01 c.141.1.1 107170 2fr1A 486 1.93e+01 1s57A 153 1.95e+01 2ck3D 482 1.96e+01 1o0sA 605 2.02e+01 c.2.1.7,c.58.1.3 86540,86541 2btoA 473 2.03e+01 1l1qA 186 2.05e+01 c.61.1.1 77653 1h8eD 482 2.07e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1e79D 482 2.11e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1kblA 873 2.14e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ofuA 320 2.17e+01 c.32.1.1,d.79.2.1 86972,86973 2b8eA 273 2.17e+01 1qhqA 140 2.17e+01 1qhqA b.6.1.1 63326 1vk9A 151 2.18e+01 c.139.1.1 108640 1vmfA 145 2.20e+01 1m6kA 251 2.20e+01 e.3.1.1 78695 1r6xA 395 2.20e+01 b.122.1.3,c.26.1.5 97167,97168 1iscA 192 2.21e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 2bcqA 335 2.22e+01 1wuaA 375 2.24e+01 1qz5A 375 2.28e+01 c.55.1.1,c.55.1.1 96614,96615 1fl2A 310 2.28e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1ykdA 398 2.30e+01 1yqgA 263 2.30e+01 1uehA 253 2.32e+01 c.101.1.1 99259 1kpeA 126 2.32e+01 1kpf d.13.1.1 37508 1fmtA 314 2.33e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1yfsA 465 2.35e+01 2gwdA 449 2.38e+01 1d4xA 375 2.39e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1xuqA 212 2.41e+01 1j6zA 376 2.42e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1o4rA 108 2.44e+01 d.93.1.1 92469 1vicA 262 2.46e+01 c.68.1.13 100756 1gteA 1025 2.47e+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 1u60A 310 2.47e+01 e.3.1.2 107692 1u7eB 154 2.48e+01 1h7wA 1025 2.48e+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 1x7dA 350 2.50e+01 2f5gA 133 2.55e+01 1vmhA 144 2.57e+01 1y4tA 322 2.61e+01 2fb5A 205 2.64e+01 2b18A 164 2.70e+01 1dusA 194 2.72e+01 1dusA c.66.1.4 34182 1tv9A 335 2.72e+01 1k8qA 377 2.75e+01 c.69.1.6 72177 1mp4A 292 2.75e+01 c.68.1.6 79376 1mpgA 282 2.81e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1dgaA 375 2.81e+01 1yagA 2d93A 134 2.85e+01 2c3zA 222 2.85e+01 1kcfA 258 2.85e+01 a.140.2.1,c.55.3.7 68434,68435 1vpbA 451 2.88e+01 1cvrA 435 2.89e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2cpl 165 2.90e+01 2cpl b.62.1.1 27420 2b81A 323 2.94e+01 1cx4A 305 2.95e+01 b.82.3.2,b.82.3.2 59099,59100 1b34B 118 2.95e+01 1b34B b.38.1.1 24797 1wnaA 131 2.96e+01 1j7dA 145 2.97e+01 1jatB d.20.1.1 62680 1nrfA 262 3.00e+01 e.3.1.1 92086 1awqA 164 3.01e+01 2cpl b.62.1.1 27461 2bhvA 246 3.02e+01 1wzvA 155 3.02e+01 1wzlA 585 3.04e+01 2aq4A 434 3.05e+01 1s14A 194 3.06e+01 d.122.1.2 98329 1eg7A 557 3.07e+01 1eg7A c.37.1.10 32241 1awsA 164 3.09e+01 2cpl b.62.1.1 27431 1vdnA 162 3.13e+01 1apyA 162 3.14e+01 1apyA d.153.1.5 42004 1eexA 554 3.17e+01 1dioA c.1.19.3 29650 2cfeA 162 3.17e+01 2a4dA 160 3.19e+01 1yndA 165 3.19e+01 1s2oA 244 3.21e+01 1jatA 155 3.25e+01 1u9aA d.20.1.1 62818 2erfA 209 3.31e+01 1qgxA 357 3.34e+01 1qgxA e.7.1.1 42973 1ka1A 357 3.42e+01 e.7.1.1 68369 1wv9A 94 3.43e+01 1p97A 114 3.49e+01 d.110.3.7 94382 1eulA 994 3.51e+01 1eulA 1puiA 210 3.54e+01 c.37.1.8 88292 1xkfA 133 3.56e+01 1ve1A 304 3.60e+01 1ex2A 189 3.63e+01 1ex2A c.51.4.2 33225 2cxaA 256 3.65e+01 1zy9A 564 3.73e+01 1su4A 994 3.73e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 2acaA 189 3.79e+01 1ofdA 1520 3.81e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1nlfA 279 3.81e+01 c.37.1.11 85850 1vr3A 191 3.82e+01 1rtqA 299 3.88e+01 c.56.5.4 97819 1j8yF 297 3.90e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1h1nA 305 4.00e+01 c.1.8.3 70855 1ypxA 375 4.00e+01 1vb3A 428 4.01e+01 2awaA 390 4.05e+01 1b1cA 181 4.06e+01 1amoA c.23.5.2 31212 2fmpA 335 4.06e+01 1f7sA 139 4.08e+01 1cof d.109.1.2 40857 1nf2A 268 4.12e+01 c.108.1.10 91849 1xreA 217 4.13e+01 1o9yA 84 4.14e+01 b.139.1.1 92692 1uurA 473 4.16e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1bu8A 452 4.17e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1m3uA 264 4.17e+01 c.1.12.8 84784 1m1nA 491 4.17e+01 c.92.2.3 78417 1z2lA 423 4.17e+01 1jyoA 130 4.24e+01 d.198.1.1 67483 1nvmA 345 4.26e+01 a.5.7.1,c.1.10.5 86249,86250 2gw2A 198 4.28e+01 2c9wA 169 4.30e+01 1i50B 1224 4.30e+01 e.29.1.1 61755 1g8fA 511 4.32e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1pmhX 185 4.32e+01 b.18.1.18 104193 1j8mF 297 4.42e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2fxuA 375 4.43e+01 2g19A 244 4.50e+01 1jflA 228 4.50e+01 c.78.2.1,c.78.2.1 71656,71657 1qq4A 198 4.54e+01 1qq4A b.47.1.1 25768 1ssxA 198 4.56e+01 b.47.1.1 98978 1vefA 395 4.60e+01 1p5dX 463 4.64e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1yphE 97 4.68e+01 1z94A 147 4.74e+01 2aeeA 211 4.78e+01 1i1iP 681 4.78e+01 1i1iP d.92.1.5 40297 1j7lA 264 4.80e+01 d.144.1.6 62697 1x0oA 119 4.80e+01 1j6oA 268 4.94e+01 c.1.9.12 77088 1plq 258 4.97e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1e79H 146 5.02e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1w94A 156 5.03e+01 1gk8I 140 5.03e+01 d.73.1.1 65242 1nm2A 317 5.06e+01 c.19.1.1,d.58.23.1 80654,80655 1i6wA 181 5.11e+01 1i6wA c.69.1.18 61859 1ispA 181 5.12e+01 c.69.1.18 76778 1pc6A 146 5.12e+01 d.262.1.1 94430 1flcA 432 5.13e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1k8kD 300 5.13e+01 d.198.2.1,d.198.2.1 68309,68310 1px5A 349 5.14e+01 a.160.1.2,d.218.1.6 95277,95278 1ry9A 145 5.19e+01 d.198.1.1 98094 1a53 247 5.19e+01 1a53 c.1.2.4 28564 2b3hA 329 5.24e+01 1bpyA 335 5.28e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1lh0A 213 5.28e+01 c.61.1.1 73896 1dceA 567 5.30e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1j8fA 323 5.30e+01 1j8fA c.31.1.5 62738 1tf9A 284 5.32e+01 2c1cA 312 5.35e+01 1ir21 140 5.35e+01 1tkjA 284 5.35e+01 1ucnA 152 5.37e+01 d.58.6.1 99183 1agjA 242 5.39e+01 1agjA b.47.1.1 25827 1i9zA 347 5.39e+01 1i9yA d.151.1.2 62102 1zfjA 491 5.41e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1nofA 383 5.43e+01 b.71.1.2,c.1.8.3 92020,92021 1zhhB 242 5.45e+01 1m6yA 301 5.45e+01 a.60.13.1,c.66.1.23 78716,78717 1qq9A 284 5.45e+01 1xjo c.56.5.4 33841 1zcbA 362 5.48e+01 1im5A 180 5.51e+01 c.33.1.3 66211 1vhxA 150 5.53e+01 c.55.3.8 100712 2hbtA 247 5.55e+01 1acf 125 5.56e+01 3nul d.110.1.1 40882 1gg6C 97 5.56e+01 5ptp 1igs 248 5.59e+01 1a53 c.1.2.4 28565 1k2yX 463 5.60e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1wpiA 133 5.63e+01 1g4wR 383 5.65e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1crzA 403 5.66e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1xjo 284 5.68e+01 1xjo c.56.5.4 33843 1at3A 247 5.73e+01 1at3A b.57.1.1 27021 1zczA 464 5.74e+01 1qisA 396 5.77e+01 1ajsA c.67.1.1 34284 1zs7A 190 5.78e+01 2cx1A 187 5.94e+01 1cvl 319 5.95e+01 1cvl c.69.1.18 34786 1jq5A 370 5.96e+01 e.22.1.2 67084 1yb0A 159 5.98e+01 1y2qA 143 5.99e+01 2c30A 321 6.02e+01 1zhaA 267 6.07e+01 1y5hA 133 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