# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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.soe.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 3eo6A 106 5.72e-02 1z47A 355 2.34e-01 1gutA 68 3.96e-01 b.40.6.1 65576 1wluA 136 4.17e-01 d.38.1.5 121015 1j1yA 136 8.38e-01 d.38.1.5 90776 3f1zA 133 8.74e-01 3kf8A 220 9.23e-01 1y6kR 214 1.16e+00 b.1.2.1,b.1.2.1 122663,122664 3e0eA 97 1.17e+00 1bkb 136 1.75e+00 1bkb 1bkbA 136 1.75e+00 b.34.5.2,b.40.4.5 24609,25341 3fvqA 359 1.92e+00 2d7vA 162 2.02e+00 d.227.1.1 146468 1ywpA 64 2.21e+00 1j1tA 233 2.29e+00 b.29.1.18 90771 1fr3A 67 2.30e+00 1fr3A b.40.6.1 25436 1ocsA 162 2.46e+00 d.189.1.1 92776 1tg0A 68 2.53e+00 1wdxA 69 2.60e+00 1a87 321 2.77e+00 1a87 2k5dA 116 2.87e+00 1y0bA 197 2.97e+00 c.61.1.1 122476 2glzA 153 3.19e+00 d.81.3.1 135348 1shfA 59 3.26e+00 1bbzA b.34.2.1 24462 1go3E 187 3.39e+00 b.40.4.5,d.230.1.1 83054,83055 1w3fA 315 3.72e+00 1jt8A 102 3.90e+00 b.40.4.5 63279 1azgB 67 4.05e+00 1bbzA b.34.2.1 24471 1khdA 345 4.39e+00 a.46.2.1,c.27.1.1 77400,77401 2zplA 97 4.67e+00 2kmcA 102 4.70e+00 2q7nA 488 4.85e+00 1o75A 415 5.00e+00 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 2je6I 251 5.15e+00 b.40.4.5,b.84.4.2,d.51.1.1 147995,147996,147997 2cqaA 95 5.26e+00 b.40.4.14 130716 2w9jA 91 5.27e+00 3k2mC 101 5.30e+00 1ddwA 120 5.36e+00 1evhA b.55.1.4 27001 2jysA 107 5.37e+00 1d7qA 143 5.40e+00 1d7qA b.40.4.5 25331 3m6sA 331 5.67e+00 2vknA 70 5.88e+00 1o7iA 119 5.96e+00 b.40.4.3 86642 2fujA 137 5.97e+00 d.38.1.1 134175 3gqnA 772 6.31e+00 1o54A 277 6.45e+00 c.66.1.13 92482 3h43A 85 6.47e+00 2bz8A 58 6.57e+00 3ehrA 222 6.66e+00 1hd3A 62 6.80e+00 b.34.2.1 65802 2elfA 370 7.09e+00 1onqA 283 7.14e+00 b.1.1.2,d.19.1.1 93365,93366 2yvlA 248 7.28e+00 2por 301 7.32e+00 2por 2porA 301 7.32e+00 f.4.3.1 43759 3kh0A 140 7.42e+00 2a2jA 246 7.50e+00 b.45.1.1 126033 1a0nB 69 8.14e+00 1bbzA b.34.2.1 24469 2q03A 138 8.22e+00 b.159.2.1 149979 3bh0A 315 8.38e+00 3id1A 95 8.80e+00 3i35A 60 9.08e+00 1j8rA 196 9.16e+00 1j8rA b.2.3.3 62745 2kk8A 84 9.27e+00 1fnf 368 9.42e+00 1fnf 2yxdA 183 9.42e+00 3ey6A 121 9.49e+00 2v5mA 388 9.53e+00 2awgA 118 9.54e+00 2k75A 106 9.60e+00 1tit 98 9.86e+00 1tit 1zkiA 133 1.01e+01 d.38.1.5 125199 1avzC 57 1.06e+01 1bbzA b.34.2.1 24467 2e2dC 180 1.08e+01 b.40.3.1 131980 2bb6A 414 1.10e+01 1hcz 252 1.11e+01 1hcz 1ibzA 112 1.12e+01 1ibzA b.6.1.4 62237 2pbeA 294 1.12e+01 a.160.1.5,d.218.1.13 149355,149356 2hdaA 64 1.21e+01 1czpA 98 1.21e+01 1awd d.15.4.1 37645 3gblA 97 1.23e+01 1yb2A 275 1.24e+01 c.66.1.13 122868 3kg9A 296 1.25e+01 1f2tA 149 1.25e+01 1f2tA c.37.1.12 32373 3cqtA 79 1.28e+01 1q72L 218 1.30e+01 b.1.1.1,b.1.1.2 96016,96017 2drmA 58 1.32e+01 2bzyA 67 1.32e+01 3gqhA 163 1.33e+01 1dt9A 437 1.34e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1uh6A 100 1.39e+01 d.15.1.1 99394 2o9uX 97 1.39e+01 d.17.1.1 138960 3klwA 98 1.40e+01 1h9sA 140 1.45e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2oqkA 117 1.47e+01 1v70A 105 1.47e+01 b.82.1.9 113555 3lhcA 100 1.48e+01 1ruzH 328 1.48e+01 b.19.1.2 97889 3gbnA 331 1.56e+01 3bpkA 206 1.58e+01 2hqxA 246 1.58e+01 b.34.9.1 136675 1ev7A 317 1.58e+01 1ev7B c.52.1.9 33315 1z94A 147 1.59e+01 d.129.3.5 124740 3dm3A 105 1.61e+01 2sicI 107 1.63e+01 3ssi d.84.1.1 40031 3en2A 101 1.64e+01 2x3wD 60 1.65e+01 3dgtA 280 1.68e+01 2iimA 62 1.69e+01 b.34.2.1 137434 1q48A 134 1.72e+01 d.224.1.2 95783 1ibyA 112 1.77e+01 1ibzA b.6.1.4 62233 2rmpA 361 1.78e+01 2rmpA b.50.1.2 26825 2rdkA 109 1.81e+01 2h36X 112 1.81e+01 2ibpA 409 1.81e+01 2jxxA 97 1.88e+01 1h6hA 143 1.89e+01 d.189.1.1 65681 1x6oA 174 1.90e+01 b.34.5.2,b.40.4.5 109493,109494 1efnA 59 1.91e+01 1bbzA b.34.2.1 24465 1oa8A 133 1.92e+01 b.145.1.1 92698 1jkgA 140 1.95e+01 d.17.4.2 66795 3gxwA 103 1.98e+01 3dm4A 115 1.99e+01 1rvtH 328 2.07e+01 b.19.1.2 97931 1sqrA 95 2.07e+01 b.43.3.3 112108 1rfkA 98 2.07e+01 1zlmA 58 2.07e+01 1vbvA 105 2.08e+01 b.34.17.1 119965 3e05A 204 2.10e+01 2oojA 141 2.12e+01 b.159.2.1 148928 1m93B 245 2.13e+01 2qazA 128 2.16e+01 1u06A 62 2.18e+01 b.34.2.1 119404 2r0hA 164 2.18e+01 2v3mA 131 2.19e+01 2v1qA 60 2.20e+01 1e8oB 106 2.21e+01 1914 d.49.1.1 38775 2ag4A 164 2.22e+01 b.95.1.1 126717 1askA 127 2.24e+01 1ounA d.17.4.2 38094 1cuk 203 2.24e+01 1hjp 1cukA 203 2.24e+01 a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2obfA 289 2.24e+01 1mjuL 219 2.26e+01 b.1.1.1,b.1.1.2 91304,91305 2rajA 392 2.28e+01 1jo8A 58 2.29e+01 b.34.2.1 71774 3hceA 289 2.31e+01 3fdrA 94 2.34e+01 3ljyA 243 2.34e+01 1bplB 294 2.35e+01 1bli b.71.1.1 27716 3bghA 236 2.36e+01 1o17A 345 2.39e+01 a.46.2.1,c.27.1.1 80765,80766 1z9zA 60 2.41e+01 2biwA 490 2.42e+01 3kojA 108 2.42e+01 3sicI 107 2.46e+01 3ssi d.84.1.1 40028 1rd8A 335 2.51e+01 b.19.1.2 97308 3df6A 99 2.52e+01 2eixA 243 2.53e+01 1rcqA 357 2.54e+01 b.49.2.2,c.1.6.1 104882,104883 1wktA 88 2.56e+01 b.11.1.2 23630 1lm8V 160 2.57e+01 b.3.3.1 74035 1lqbC 162 2.58e+01 b.3.3.1 74186 1jsmA 325 2.61e+01 b.19.1.2 63264 3iq2A 138 2.62e+01 1f0cA 305 2.64e+01 1c8oA e.1.1.1 42676 2glwA 92 2.65e+01 3l0xB 94 2.65e+01 1molA 94 2.66e+01 1molA d.17.1.1 37988 3heiB 132 2.67e+01 1waaA 93 2.81e+01 2fblA 153 2.83e+01 d.63.1.2 133249 3bf2A 152 2.84e+01 1rv0H 328 2.86e+01 b.19.1.2 97895 3baeL 218 2.88e+01 1x2kA 68 2.89e+01 1mwqA 101 2.91e+01 d.58.4.7 91481 2h9uA 102 2.91e+01 1ia9A 280 2.92e+01 1ia9A d.144.1.5 62113 2j5aA 110 2.94e+01 d.58.14.1 147886 1nnvA 110 2.96e+01 d.17.7.1 92012 1xgyL 216 2.97e+01 2a1hA 365 2.98e+01 e.17.1.1 125997 1bnzA 64 2.99e+01 1azpA b.34.13.1 37468 2an1A 292 3.01e+01 2a15A 139 3.02e+01 d.17.4.3 125973 1mogA 67 3.03e+01 d.230.2.1 85034 3a4rA 79 3.03e+01 1yn8A 59 3.04e+01 1noaA 113 3.06e+01 b.1.7.1 22208 3mhsA 476 3.07e+01 3g0mA 141 3.13e+01 2cwrA 103 3.15e+01 2de0X 526 3.15e+01 3fn2A 106 3.17e+01 1zn8A 180 3.19e+01 c.61.1.1 125376 1iz6A 138 3.19e+01 b.34.5.2,b.40.4.5 76976,76977 2uubL 135 3.22e+01 b.40.4.5 139943 3djwA 99 3.22e+01 2k89A 80 3.22e+01 3fkeA 129 3.23e+01 1br9 194 3.24e+01 1br9 1a78A 134 3.24e+01 1c1lA b.29.1.3 24212 1w15A 153 3.26e+01 b.7.1.2 109041 1o6aA 96 3.27e+01 b.139.1.1 92562 1p3hA 99 3.30e+01 b.35.1.1 87734 1l1qA 186 3.30e+01 c.61.1.1 77653 3il8A 72 3.30e+01 d.9.1.1 37356 1v8hA 107 3.32e+01 b.1.18.19 119870 2kd2A 94 3.35e+01 1idsA 207 3.36e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1mppA 361 3.40e+01 b.50.1.2 26856 3a3oB 64 3.41e+01 2v43A 303 3.44e+01 3c0cA 73 3.47e+01 3hfiA 170 3.51e+01 1ekfA 365 3.58e+01 1ekfA e.17.1.1 59445 1vcbC 160 3.62e+01 1vcbC b.3.3.1 22535 3httA 324 3.64e+01 1wy7A 207 3.65e+01 c.66.1.32 121433 2g72A 289 3.66e+01 c.66.1.15 134724 2f5tX 233 3.68e+01 b.38.5.1,d.136.1.5 146996,146997 1ruyH 328 3.69e+01 b.19.1.2 97883 2gpcA 194 3.71e+01 2v5sA 394 3.75e+01 1jmcA 246 3.78e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1wocA 103 3.82e+01 2bzgA 232 3.84e+01 c.66.1.36 129559 1tx4B 178 3.85e+01 1ctqA c.37.1.8 32045 1vc3B 97 3.85e+01 1h5bA 113 3.86e+01 1tvdA b.1.1.1 60638 2whdA 351 3.89e+01 3db3A 161 3.91e+01 3f3bA 126 3.93e+01 2ggrA 76 3.96e+01 3knyA 218 3.96e+01 2kcpA 98 4.01e+01 1ai1L 215 4.01e+01 8fabA b.1.1.1,b.1.1.2 19882,20978 2d6fA 435 4.03e+01 b.38.3.1,c.88.1.1 131303,131304 3goeA 82 4.04e+01 2bpqA 373 4.06e+01 3gbmA 334 4.12e+01 1fnaA 91 4.12e+01 b.1.2.1 21971 3hcaA 289 4.13e+01 1fna 93 4.14e+01 1fnf 2yv8A 164 4.18e+01 1ae6L 219 4.21e+01 8fabA b.1.1.1,b.1.1.2 20210,21222 2pwyA 258 4.22e+01 1h5bB 113 4.24e+01 b.1.1.1 60639 3cc1A 433 4.29e+01 1ipcA 217 4.30e+01 d.86.1.1 71257 1lylA 504 4.30e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 3bevA 274 4.33e+01 2j6fA 62 4.34e+01 1ad9A 219 4.36e+01 8fabA b.1.1.1,b.1.1.2 20214,21226 3g5pA 183 4.37e+01 1axiB 236 4.37e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 2co3A 137 4.38e+01 b.2.3.2 130665 2otuA 115 4.45e+01 1a22B 238 4.47e+01 1axiB b.1.2.1,b.1.2.1 22003,22004 1ru7A 327 4.51e+01 b.19.1.2 97837 2d1xA 66 4.54e+01 1hjdA 101 4.55e+01 b.34.2.1 65846 3i4hX 273 4.55e+01 1k42A 168 4.59e+01 b.18.1.14 72032 2uubJ 105 4.60e+01 d.58.15.1 139941 1aonO 97 4.60e+01 b.35.1.1 24642 3hi0A 508 4.61e+01 2oynA 146 4.63e+01 b.43.5.2 149067 3a3nB 67 4.64e+01 3l6vA 370 4.66e+01 2p3hA 101 4.69e+01 d.145.1.4 149177 1khoA 370 4.73e+01 a.124.1.1,b.12.1.3 72489,72490 3d82A 102 4.76e+01 1ywhA 313 4.76e+01 g.7.1.3,g.7.1.3,g.7.1.3 145925,145926,145927 2z30B 65 4.81e+01 1z3qA 200 4.83e+01 1qr4B 186 4.88e+01 1qr4B b.1.2.1,b.1.2.1 21988,21989 2f0xA 148 4.89e+01 d.38.1.5 132673 1jb2A 127 4.91e+01 d.17.4.2 71624 2ofsA 75 4.93e+01 2h88A 621 4.95e+01 2rcfA 91 4.97e+01 b.40.15.1 151885 2zu1A 183 5.00e+01 1hnnA 282 5.00e+01 c.66.1.15 65895 2vbuA 136 5.01e+01 b.43.5.2 152911 1d9nA 75 5.01e+01 1d9nA d.10.1.3 37486 1j53A 186 5.02e+01 c.55.3.5 77076 1bf5A 545 5.03e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2ou5A 175 5.03e+01 1p9lA 245 5.05e+01 c.2.1.3,d.81.1.3 94393,94394 1d0dA 60 5.19e+01 1kigI g.8.1.2 44566 3bwuF 142 5.24e+01 1v1qA 134 5.24e+01 b.40.4.3 113490 3e1eA 141 5.28e+01 2w5eA 163 5.37e+01 1ndh 272 5.38e+01 1ndh 2fyqA 194 5.40e+01 2vd8A 391 5.41e+01 2a73B 991 5.42e+01 2pbcA 102 5.43e+01 3fhwA 115 5.46e+01 1sa3A 262 5.46e+01 c.52.1.23 105400 2d6mA 159 5.49e+01 1bmlC 362 5.51e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1igqA 62 5.60e+01 b.34.1.3 66130 1bkzA 135 5.60e+01 1a3k b.29.1.3 24202 1qlyA 58 5.61e+01 1bbzA b.34.2.1 24530 1l3aA 228 5.61e+01 d.18.1.2 73531 3hhrB 203 5.62e+01 1axiB b.1.2.1,b.1.2.1 22005,22006 2nttA 217 5.65e+01 1mzgA 146 5.73e+01 d.224.1.1 79696 1rvxA 327 5.75e+01 b.19.1.2 97937 3huiA 126 5.77e+01 2iubA 363 5.79e+01 d.328.1.1,f.17.3.1 137669,137670 1k52A 72 5.86e+01 d.15.7.1 68148 2jtmA 60 5.88e+01 2j8bA 79 5.88e+01 g.7.1.3 147908 1j2gA 319 5.89e+01 d.96.1.4,d.96.1.4 103824,103825 2qc5A 300 5.90e+01 3dni 260 5.92e+01 3dni 1cmxA 236 5.98e+01 1uch d.3.1.6 37130 2oq0A 206 6.01e+01 b.40.16.1,b.40.16.1 148970,148971 1qfjA 232 6.03e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1o5uA 101 6.05e+01 b.82.1.8 92518 1umkA 275 6.07e+01 b.43.4.2,c.25.1.1 113312,113313 2pii 112 6.11e+01 2pii 3ivrA 509 6.13e+01 1gzqA 300 6.14e+01 b.1.1.2,d.19.1.1 70818,70819 3kioC 166 6.15e+01 1a4kA 217 6.15e+01 8fabA b.1.1.1,b.1.1.2 20236,21248 2p4bA 295 6.16e+01 1drw 273 6.20e+01 1drw 1drwA 273 6.20e+01 c.2.1.3,d.81.1.3 30057,39972 3jxsA 174 6.23e+01 2joxA 106 6.24e+01 3ejhA 93 6.25e+01 1o0iA 138 6.32e+01 d.38.1.5 86532 1rd8B 182 6.32e+01 h.3.1.1 97309 1lpjA 133 6.34e+01 b.60.1.2 78123 2h26A 291 6.35e+01 b.1.1.2,d.19.1.1 135990,135991 3ku3A 327 6.35e+01 1lj5A 379 6.35e+01 e.1.1.1 73928 1ar0A 127 6.37e+01 1ounA d.17.4.2 38092 1ktjA 129 6.39e+01 b.1.18.7 72974 2rprA 87 6.40e+01 2k8hA 110 6.43e+01 1nfjA 89 6.45e+01 d.68.6.1 91866 2eisA 133 6.52e+01 1q33A 292 6.53e+01 d.113.1.1 95657 1i7pA 274 6.54e+01 b.43.4.2,c.25.1.1 66048,66049 2va0A 131 6.54e+01 1aw8B 91 6.58e+01 1aw8B 3k85A 357 6.59e+01 1yvcA 70 6.60e+01 b.40.4.12 124094 2wxuA 370 6.62e+01 1kawA 135 6.65e+01 3ullA b.40.4.3 25288 2cmgA 262 6.66e+01 3maoA 105 6.70e+01 1klo 162 6.70e+01 1klo 1kloA 162 6.70e+01 g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 2bazA 142 6.72e+01 1oa4A 222 6.73e+01 b.29.1.11 86731 1ncwL 219 6.75e+01 b.1.1.1,b.1.1.2 85557,85558 1mngA 203 6.77e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1tw3A 360 6.79e+01 a.4.5.29,c.66.1.12 107373,107374 2czvC 120 6.81e+01 d.58.59.1 145059 1u3oA 82 6.88e+01 2i82A 217 6.97e+01 2zz8A 241 6.99e+01 1v05A 96 7.01e+01 b.1.18.10 113465 3ea6A 219 7.08e+01 1fm2B 520 7.08e+01 1fm2B 1y0mA 61 7.09e+01 2vt8A 153 7.10e+01 1ny4A 82 7.11e+01 b.40.4.5 92316 2gfaA 119 7.12e+01 b.34.9.1,b.34.9.1 135089,135090 2x57A 116 7.16e+01 1bf4A 63 7.17e+01 1azpA b.34.13.1 37461 1bdo 80 7.17e+01 1bdo 1bdoA 80 7.17e+01 b.84.1.1 28214 1k2eA 156 7.17e+01 d.113.1.1 72010 3fdyA 623 7.18e+01 3a3pB 69 7.20e+01 1yezA 68 7.25e+01 b.40.4.12 123026 3kzhA 328 7.26e+01 2dy0A 190 7.36e+01 2v6oA 596 7.41e+01 1jsdA 319 7.41e+01 b.19.1.2 63258 2bsfA 176 7.41e+01 2wxfA 940 7.43e+01 1sc0A 138 7.44e+01 d.38.1.5 98796 3iesA 551 7.45e+01 3c8mA 331 7.48e+01 2kcaA 109 7.49e+01 3h4kA 598 7.51e+01 2qklA 127 7.54e+01 2wgoA 98 7.55e+01 1tzzA 392 7.56e+01 c.1.11.2,d.54.1.1 112896,112897 1aocA 175 7.58e+01 1aocA g.17.1.5 44817 1zuuA 58 7.59e+01 b.34.2.1 125688 1pqhA 143 7.63e+01 b.52.2.1 95017 3eg3A 63 7.64e+01 1fvuB 125 7.65e+01 1ixxB d.169.1.1 42346 1boy 219 7.66e+01 1boy 2ibxA 340 7.67e+01 b.19.1.2 137209 2dleA 104 7.73e+01 3bg6A 623 7.75e+01 2jk8A 302 7.82e+01 3lw3A 145 7.82e+01 2z2nA 299 7.85e+01 2f5vA 595 7.90e+01 c.3.1.2,d.16.1.1 133010,133011 1kjvA 284 7.92e+01 b.1.1.2,d.19.1.1 77421,77422 2jheA 190 7.92e+01 1jjgA 102 7.93e+01 b.40.4.5 71696 1lo7A 141 7.97e+01 d.38.1.1 74144 3ezmA 101 7.98e+01 3ezmA b.89.1.1 28395 3cfuA 159 7.99e+01 1prxA 224 8.00e+01 1prxA c.47.1.10 33076