# List of top-scoring protein chains for t04-100-30-str2-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 2.73e-24 1yvoA 172 4.56e-23 2ge3A 170 4.85e-23 2bl1A 172 3.37e-22 1vhsA 175 2.48e-21 d.108.1.1 100698 1tiqA 180 5.25e-21 d.108.1.1 107010 2ae6A 166 1.04e-20 2fe7A 166 4.06e-20 1nslA 184 2.88e-19 d.108.1.1 86137 2cy2A 174 3.78e-19 2beiA 170 6.22e-19 1wwzA 159 7.21e-18 1z4eA 153 1.12e-17 1u6mA 199 2.25e-17 1s7kA 182 5.95e-17 2b5gA 171 6.56e-17 1s3zA 165 7.33e-17 d.108.1.1 105250 1gheA 177 1.32e-16 d.108.1.1 76222 2fckA 181 3.13e-16 2fl4A 149 3.29e-16 1i1dA 161 2.39e-15 1i21A d.108.1.1 61526 1i12A 160 3.20e-15 1i21A d.108.1.1 61515 1y9kA 157 3.62e-15 1yreA 197 5.46e-15 1qsmA 152 6.92e-15 1qsmA d.108.1.1 40808 1on0A 158 8.88e-15 d.108.1.1 87095 1qsoA 149 1.38e-14 1qsmA d.108.1.1 40812 1yvkA 163 6.57e-14 1b87A 181 7.94e-14 1b87A d.108.1.1 40797 1vkcA 158 8.17e-14 2a4nA 182 8.47e-14 1n71A 180 1.73e-13 d.108.1.1 85370 1cjwA 166 2.34e-13 1cjwA d.108.1.1 40818 1mk4A 157 3.78e-13 d.108.1.1 84979 2c27A 315 5.43e-12 1y9wA 140 7.00e-12 1p0hA 318 1.72e-11 d.108.1.1 93866 1q2yA 140 1.77e-11 d.108.1.1 95655 2fsrA 195 1.78e-11 2atrA 138 2.12e-11 2bswA 146 2.34e-11 1z4rA 168 2.71e-11 1qstA 160 3.85e-11 1yghA d.108.1.1 40804 1y7rA 133 5.98e-11 1yx0A 159 7.85e-11 2ganA 190 1.43e-10 2g3aA 152 1.87e-10 1bo4A 168 1.88e-10 1bo4A d.108.1.1 40798 1yk3A 210 3.54e-10 1xebA 150 8.89e-10 1yghA 164 1.41e-09 1yghA d.108.1.1 40802 2aj6A 159 2.13e-09 1sqhA 312 2.41e-09 d.108.1.5 98966 1m4iA 181 1.25e-08 d.108.1.1 74457 2d4pA 141 6.59e-08 1bob 320 1.59e-06 1bob d.108.1.1 40816 1yleA 342 2.25e-05 1iicA 422 4.19e-05 1nmtA d.108.1.2,d.108.1.2 62422,62423 1kzfA 230 3.88e-04 d.108.1.3 73354 1xmtA 103 8.07e-04 1fy7A 278 9.92e-04 1fy7A d.108.1.1 40817 1ne9A 335 3.37e-03 d.108.1.4,d.108.1.4 91839,91840 2givA 295 4.56e-03 1svjA 156 8.57e-03 d.220.1.1 106049 1ro5A 201 1.97e-02 d.108.1.3 105023 1lkdA 297 5.34e-02 d.32.1.3,d.32.1.3 78059,78060 2arhA 203 5.47e-02 1pixA 587 5.84e-02 c.14.1.4 94708 1han 297 6.49e-02 1han d.32.1.3,d.32.1.3 38506,38507 2b8eA 273 8.38e-02 1f1uA 323 9.06e-02 d.32.1.3,d.32.1.3 83200,83201 1pbjA 125 2.66e-01 d.37.1.1,d.37.1.1 94414,94415 1kw3B 292 2.76e-01 d.32.1.3,d.32.1.3 77549,77550 1to6A 371 2.89e-01 c.141.1.1 107170 1on3A 523 3.18e-01 c.14.1.4,c.14.1.4 87107,87108 1ss4A 153 3.89e-01 d.32.1.6 105976 1o50A 157 4.40e-01 d.37.1.1,d.37.1.1 92478,92479 1lrzA 426 4.50e-01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1afwA 393 4.68e-01 1afwA c.95.1.1,c.95.1.1 35900,35901 1f1xA 322 5.20e-01 d.32.1.3,d.32.1.3 83208,83209 1vicA 262 7.78e-01 c.68.1.13 100756 1kllA 130 8.19e-01 d.32.1.2 72720 2d5cA 263 8.23e-01 2cxaA 256 8.32e-01 1fmtA 314 8.58e-01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1pvmA 184 8.71e-01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wxdA 263 9.01e-01 1xtmA 175 9.52e-01 2cy0A 263 9.65e-01 1lqpA 135 9.80e-01 d.32.1.2 78151 1nkiA 135 9.80e-01 d.32.1.2 91941 1xtlA 175 1.17e+00 1su4A 994 1.17e+00 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1r6xA 395 1.28e+00 b.122.1.3,c.26.1.5 97167,97168 1s14A 194 1.34e+00 d.122.1.2 98329 1edzA 320 1.41e+00 1ee9A c.2.1.7,c.58.1.2 30287,33935 1lx7A 253 1.46e+00 c.56.2.1 74329 1wpgA 994 1.58e+00 1rxyA 253 1.58e+00 c.56.2.1 98065 1s4iA 175 1.68e+00 1rfmA 344 1.73e+00 c.122.1.1 97385 1xbfA 140 1.79e+00 d.273.1.1 109538 1eulA 994 1.87e+00 1eulA 1o0wA 252 1.92e+00 a.149.1.1,d.50.1.1 80751,80752 2cfeA 162 1.95e+00 1ykdA 398 2.06e+00 1rkuA 206 2.13e+00 c.108.1.11 97627 1shdA 107 2.15e+00 1fmk d.93.1.1 40440 1hh1A 143 2.31e+00 1gefA c.52.1.18 61036 1xkfA 133 2.36e+00 2gwdA 449 2.44e+00 1qflA 389 2.55e+00 1afwA c.95.1.1,c.95.1.1 35908,35909 1qysA 106 2.56e+00 k.41.1.1 96603 1m4tA 392 2.63e+00 c.95.1.1,c.95.1.1 78617,78618 1oltA 457 2.64e+00 c.1.28.2 93334 1uyrA 737 2.67e+00 c.14.1.4,c.14.1.4 100188,100189 1g8fA 511 2.68e+00 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1yphE 97 2.74e+00 1m3kA 392 2.75e+00 c.95.1.1,c.95.1.1 78565,78566 2cpl 165 2.76e+00 2cpl b.62.1.1 27420 1yndA 165 2.77e+00 1cvrA 435 2.84e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1qq4A 198 2.85e+00 1qq4A b.47.1.1 25768 1ssxA 198 2.85e+00 b.47.1.1 98978 2b18A 164 2.97e+00 1vdmA 153 2.97e+00 1ojrA 274 3.07e+00 c.74.1.1 93147 1s57A 153 3.18e+00 1v2xA 194 3.20e+00 c.116.1.1 100274 1gteA 1025 3.22e+00 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 1zyoA 191 3.24e+00 1vb3A 428 3.25e+00 1zmaA 118 3.28e+00 1e79D 482 3.33e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2f46A 156 3.43e+00 1st9A 143 3.50e+00 c.47.1.10 98987 1v9nA 360 3.56e+00 1jflA 228 3.59e+00 c.78.2.1,c.78.2.1 71656,71657 1npk 154 3.61e+00 1npk d.58.6.1 39099 1vdnA 162 3.69e+00 1wzlA 585 3.85e+00 1zejA 293 3.88e+00 1awqA 164 3.92e+00 2cpl b.62.1.1 27461 1qgxA 357 3.98e+00 1qgxA e.7.1.1 42973 1v93A 296 4.06e+00 c.1.23.1 100532 1xdzA 240 4.09e+00 1ka1A 357 4.13e+00 e.7.1.1 68369 1g4wR 383 4.50e+00 1g4uS a.24.11.1,c.45.1.2 16644,32692 1y81A 138 4.50e+00 1o9yA 84 4.53e+00 b.139.1.1 92692 2b81A 323 4.60e+00 1fjgK 129 4.65e+00 1fjfK c.55.4.1 33733 1zo0A 126 4.97e+00 1gg6C 97 5.00e+00 5ptp 1hqsA 423 5.01e+00 1iso c.77.1.1 61154 1qcsA 211 5.06e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1ofuA 320 5.11e+00 c.32.1.1,d.79.2.1 86972,86973 1y5hA 133 5.12e+00 1kyfA 247 5.40e+00 b.1.10.1,d.105.1.1 73220,73221 1p5dX 463 5.57e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1y1uA 585 5.72e+00 1dik 874 5.77e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1awsA 164 5.78e+00 2cpl b.62.1.1 27431 1qtsA 247 5.84e+00 1qtsA b.1.10.1,d.105.1.1 22313,40789 1w2xA 758 5.93e+00 c.14.1.4,c.14.1.4 109134,109135 1b34B 118 6.13e+00 1b34B b.38.1.1 24797 1ni9A 338 6.14e+00 e.7.1.2 85739 1x7dA 350 6.20e+00 1h8eD 482 6.24e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1wd5A 208 6.44e+00 1yemA 179 6.49e+00 4pfk 319 6.54e+00 3pfk c.89.1.1 35582 1cvl 319 6.68e+00 1cvl c.69.1.18 34786 1w94A 156 6.79e+00 1g2qA 187 7.03e+00 c.61.1.1 65117 1qipA 183 7.04e+00 1qipA d.32.1.1 38470 1eg7A 557 7.14e+00 1eg7A c.37.1.10 32241 1vefA 395 7.28e+00 1o6aA 96 7.31e+00 b.139.1.1 92562 2f9sA 151 7.36e+00 1jvbA 347 7.37e+00 b.35.1.2,c.2.1.1 77181,77182 1d5tA 433 7.38e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1faaA 124 7.39e+00 1erv c.47.1.1 32738 1fm0E 150 7.53e+00 1fmaE d.41.5.1 38629 1f9mA 112 7.61e+00 1erv c.47.1.1 32736 1iznB 277 7.73e+00 e.43.1.2 83848 1eexA 554 7.77e+00 1dioA c.1.19.3 29650 1zcoA 262 7.89e+00 1xnzA 264 7.95e+00 1mpgA 282 7.98e+00 1mpgA a.96.1.3,d.129.1.2 18747,41296 1j7dA 145 8.13e+00 1jatB d.20.1.1 62680 1vmaA 306 8.14e+00 a.24.13.1,c.37.1.10 108887,108888 1hi9A 274 8.18e+00 1hi9A c.99.1.1 61063 2bl9A 238 8.25e+00 1aop 497 8.25e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1wruA 379 8.29e+00 1gjwA 637 8.45e+00 b.71.1.1,c.1.8.1 60582,60583 1shbA 104 8.60e+00 1fmk d.93.1.1 40425 2tbs 222 8.66e+00 5ptp b.47.1.2 26009 1h7wA 1025 8.68e+00 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 2a4dA 160 8.71e+00 1ecrA 309 9.01e+00 1ecrA e.2.1.1 42678 1m6kA 251 9.29e+00 e.3.1.1 78695 1ys1X 320 9.32e+00 1wnaA 131 9.51e+00 1f7uA 607 9.68e+00 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1c24A 263 9.70e+00 1c24A d.127.1.1 41148 1m1nA 491 9.74e+00 c.92.2.3 78417 1ecfA 504 9.77e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1i1iP 681 9.82e+00 1i1iP d.92.1.5 40297 1vmfA 145 1.00e+01 1xmzA 241 1.01e+01 2ck3D 482 1.02e+01 1ut7A 171 1.02e+01 b.143.1.1 99906 2aq4A 434 1.02e+01 1usyA 275 1.04e+01 1l3kA 196 1.05e+01 d.58.7.1,d.58.7.1 73539,73540 1k2yX 463 1.06e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1hv9A 456 1.06e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1mgpA 313 1.07e+01 c.119.1.1 79098 1ofdA 1520 1.09e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1g8lA 411 1.09e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1pmhX 185 1.09e+01 b.18.1.18 104193 1cg2A 393 1.12e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1pq4A 291 1.12e+01 c.92.2.2 94995 1nxuA 333 1.15e+01 c.122.1.1 86389 2gw2A 198 1.16e+01 1e1aA 314 1.18e+01 1e1aA b.68.6.1 59155 1o13A 136 1.19e+01 c.55.5.1 80762 1sqiA 393 1.20e+01 d.32.1.3,d.32.1.3 105914,105915 1pjxA 314 1.21e+01 b.68.6.1 104167 2awpA 198 1.22e+01 1vhxA 150 1.25e+01 c.55.3.8 100712 1ne6A 283 1.25e+01 b.82.3.2,b.82.3.2 91831,91832 1u14A 172 1.27e+01 c.51.4.3 107579 1kblA 873 1.29e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2a50B 168 1.30e+01 1ti6A 875 1.30e+01 b.52.2.2,c.81.1.1 106974,106975 1molA 94 1.31e+01 1molA d.17.1.1 37988 1s2oA 244 1.31e+01 1w5fA 353 1.32e+01 1e19A 314 1.32e+01 1b7bA c.73.1.1 34967 2blcA 238 1.32e+01 2a5kA 307 1.35e+01 1a58 177 1.35e+01 2cpl b.62.1.1 27495 1uehA 253 1.35e+01 c.101.1.1 99259 1q2wA 308 1.36e+01 b.47.1.4 88355 2cfuA 658 1.36e+01 1cr5A 189 1.37e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1nlfA 279 1.38e+01 c.37.1.11 85850 2amdA 311 1.38e+01 1dusA 194 1.38e+01 1dusA c.66.1.4 34182 2ggcA 263 1.39e+01 1i0vA 104 1.41e+01 9rnt d.1.1.4 36054 1x1iA 752 1.42e+01 1vmhA 144 1.42e+01 1dceA 567 1.44e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1erzA 303 1.44e+01 1erzA d.160.1.2 59498 1r7aA 504 1.44e+01 b.71.1.1,c.1.8.1 97192,97193 1uf5A 303 1.45e+01 d.160.1.2 107808 1zy9A 564 1.45e+01 1q7bA 244 1.46e+01 c.2.1.2 96026 1rh9A 373 1.46e+01 1tljA 213 1.46e+01 d.282.1.1 107126 1rypC 244 1.46e+01 1rypC d.153.1.4 41934 2ax4A 198 1.47e+01 1v8cA 168 1.49e+01 d.15.3.1,d.129.5.1 100495,100496 1gpl 432 1.49e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1yocA 147 1.49e+01 1uwvA 433 1.50e+01 b.40.4.12,c.66.1.40 100128,100129 1jnyA 435 1.51e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1ppfE 218 1.52e+01 1a7s b.47.1.2 26234 1zczA 464 1.55e+01 1f2dA 341 1.56e+01 1f2dA c.79.1.1 35298 2b3hA 329 1.57e+01 1qo7A 394 1.57e+01 1qo7A c.69.1.11 34697 1s4bP 674 1.58e+01 d.92.1.5 105252 2f9nA 245 1.59e+01 1cx4A 305 1.60e+01 b.82.3.2,b.82.3.2 59099,59100 1wk2A 121 1.60e+01 1th7A 81 1.65e+01 1hj8A 222 1.66e+01 b.47.1.2 65844 1vhmA 195 1.67e+01 d.110.2.1 100691 1jc4A 148 1.68e+01 1jc4A d.32.1.4 62863 1vp8A 201 1.68e+01 1oalA 151 1.69e+01 b.1.8.1 86739 2anwA 241 1.69e+01 1tib 269 1.70e+01 3tgl c.69.1.17 34738 1zcxA 178 1.70e+01 2fhxA 246 1.71e+01 2acaA 189 1.74e+01 1h75A 81 1.77e+01 1h75A c.47.1.1 60716 1g8yA 279 1.78e+01 1g8yA c.37.1.11 32302 1fxjA 331 1.79e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 2cxhA 217 1.80e+01 2fyxA 143 1.84e+01 1xuqA 212 1.86e+01 1y2qA 143 1.87e+01 1vk9A 151 1.88e+01 c.139.1.1 108640 2fvgA 340 1.89e+01 2bhmA 164 1.91e+01 1zh5A 195 1.92e+01 1jg5A 83 1.92e+01 d.205.1.1 66666 1an9A 340 1.92e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1wucA 250 1.92e+01 1o12A 376 1.95e+01 b.92.1.5,c.1.9.10 80758,80759 2bjvA 265 1.95e+01 1e42A 258 1.96e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 1p97A 114 1.98e+01 d.110.3.7 94382 1ex7A 186 2.04e+01 1gky c.37.1.1 59537 2pfkA 320 2.04e+01 3pfk c.89.1.1 35577 1txlA 215 2.05e+01 b.60.1.4 107429 1whtB 153 2.06e+01 1whtB 1whsB 153 2.07e+01 1whtB 1l3iA 192 2.08e+01 c.66.1.22 77676 1zwyA 185 2.08e+01 1h7eA 245 2.09e+01 c.68.1.13 60717 1yaiA 151 2.11e+01 1yaiA b.1.8.1 22289 1xvaA 292 2.15e+01 1xvaA c.66.1.5 34183 1eyqA 222 2.15e+01 1eypA d.36.1.1 38534 1nd4A 264 2.17e+01 d.144.1.6 91815 1q9iA 571 2.17e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1ihgA 370 2.17e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1o0sA 605 2.17e+01 c.2.1.7,c.58.1.3 86540,86541 1ucnA 152 2.18e+01 d.58.6.1 99183 2bitX 165 2.18e+01 1u60A 310 2.19e+01 e.3.1.2 107692 1iscA 192 2.20e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1wdtA 665 2.20e+01 1pfkA 320 2.21e+01 3pfk c.89.1.1 35575 1gox 370 2.21e+01 1gox c.1.4.1 28607 1wy7A 207 2.22e+01 2b4yA 271 2.24e+01 1q06A 135 2.26e+01 a.6.1.3 95493 1wcv1 257 2.26e+01 1rypH 205 2.26e+01 d.153.1.4 41876 1u7eB 154 2.27e+01 1plq 258 2.27e+01 1plq d.131.1.2,d.131.1.2 41388,41389 2bd0A 244 2.28e+01 1t95A 240 2.29e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1flcA 432 2.29e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1wd6A 123 2.29e+01 1nrfA 262 2.30e+01 e.3.1.1 92086 1zybA 232 2.31e+01 1qhxA 178 2.32e+01 1qhsA c.37.1.3 31936 1louA 101 2.32e+01 1ris d.58.14.1 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