# 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.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 3ckaA 320 8.45e-02 1h6fA 193 1.46e-01 b.2.5.4 70901 2q9kA 151 1.56e-01 1x1iA 752 3.63e-01 a.102.3.2,b.24.1.1,b.30.5.2 121584,121585,121586 1zx5A 300 3.64e-01 b.82.1.3 125763 2ihoA 293 4.88e-01 b.42.2.1,d.3.1.18 147681,147682 3ef2A 293 5.32e-01 3ejjX 289 6.28e-01 1j0mA 752 6.88e-01 a.102.3.2,b.24.1.1,b.30.5.2 83910,83911,83912 1c3hA 137 7.23e-01 b.22.1.1 90405 1khoA 370 1.30e+00 a.124.1.1,b.12.1.3 72489,72490 3hbzA 342 1.40e+00 2c9oA 456 1.56e+00 1eybA 471 1.69e+00 1ey2A b.82.1.4 28115 2wxuA 370 1.84e+00 1ca1 370 1.93e+00 1ca1 1ca1A 370 1.93e+00 a.124.1.1,b.12.1.3 19340,23648 3e8pA 164 2.21e+00 2hkdA 320 2.40e+00 3cslA 865 2.53e+00 2dtcA 126 2.79e+00 2v8qA 157 3.05e+00 d.129.6.2 152781 2i5vO 251 3.10e+00 2pooA 355 3.19e+00 1qlgA b.68.3.1 27626 2gopA 347 3.29e+00 1qlgA 355 3.39e+00 1qlgA b.68.3.1 27627 1p4uA 153 3.44e+00 b.1.10.2 87780 2odjA 428 3.45e+00 3gvjA 670 3.86e+00 1c28A 135 3.96e+00 1c28A b.22.1.1 23857 1h6lA 353 4.04e+00 b.68.3.1 60687 2yqzA 263 4.19e+00 3ju4A 670 4.20e+00 2oy7A 320 4.34e+00 3fhhA 640 4.39e+00 1xovA 326 4.51e+00 b.34.11.4,c.56.5.6 122206,122207 3gvkA 670 4.53e+00 2wozA 318 4.57e+00 2hb0A 369 5.09e+00 3h6jA 438 5.49e+00 1v0eA 666 5.68e+00 b.68.1.2,b.108.1.3 113466,113467 2vzpA 127 5.74e+00 2cg4A 152 6.09e+00 a.4.5.32,d.58.4.2 130417,130418 2qtdA 105 6.53e+00 2dyiA 162 6.57e+00 2asbA 251 6.84e+00 b.40.4.5,d.52.3.1,d.52.3.1 127244,127245,127246 1ospO 257 6.89e+00 1ospO b.76.1.1 27971 1t16A 427 6.91e+00 f.4.3.4 106242 3greA 437 7.29e+00 1kn3A 183 7.42e+00 b.17.1.1 72764 3drnA 161 7.67e+00 2r2yA 153 7.73e+00 2v8pA 271 7.80e+00 1qg3A 195 7.83e+00 1qg3A b.1.2.1,b.1.2.1 21993,21994 2g8cO 251 7.95e+00 1guiA 155 8.17e+00 b.18.1.14 76351 1b78A 193 8.20e+00 1b78A c.51.4.1 33221 3dzmA 214 8.33e+00 2w38A 438 9.15e+00 3f7eA 131 9.25e+00 1qfmA 710 9.25e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 2q78A 153 9.47e+00 d.38.1.7 150076 3aagA 291 9.52e+00 1dleA 298 9.63e+00 1dleA b.47.1.2 26312 1b7aA 186 9.90e+00 1a44 b.17.1.1 23705 2f2fC 186 9.91e+00 b.42.2.1 132812 1h2wA 710 9.95e+00 b.69.7.1,c.69.1.4 76596,76597 1jsmA 325 1.01e+01 b.19.1.2 63264 1sh8A 154 1.03e+01 d.38.1.5 105549 1wfwA 74 1.04e+01 b.34.2.1 114595 2p26A 280 1.04e+01 2htaA 309 1.08e+01 3itaA 352 1.16e+01 1bavA 309 1.18e+01 1aye c.56.5.1 33806 1k0rA 366 1.23e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 3g7mA 151 1.24e+01 1o6gA 710 1.26e+01 b.69.7.1,c.69.1.4 81087,81088 1e8nA 710 1.26e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 3dwnA 427 1.31e+01 2o31A 67 1.31e+01 1yuwA 554 1.31e+01 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 2hazA 105 1.33e+01 b.1.2.1 136303 1behA 187 1.37e+01 1a44 b.17.1.1 23700 1j24A 143 1.38e+01 c.52.1.20 84008 1pkhA 204 1.38e+01 b.85.4.1 94832 1o0wA 252 1.40e+01 a.149.1.1,d.50.1.1 80751,80752 1rwiA 270 1.42e+01 b.68.9.1 97987 2c36A 285 1.45e+01 2o9sA 67 1.46e+01 2f57A 317 1.47e+01 2klaA 106 1.50e+01 2bh9A 489 1.50e+01 2zklA 369 1.50e+01 1ze3D 125 1.55e+01 b.167.1.1 124976 1nwpA 128 1.57e+01 1nwpA b.6.1.1 23011 2v0uA 146 1.59e+01 1efcA 393 1.59e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 2kieA 124 1.60e+01 2wb7A 526 1.61e+01 2p5iA 288 1.65e+01 d.104.1.3 149248 2qjvA 270 1.70e+01 1jmaA 290 1.70e+01 b.1.1.1 63177 1mhxA 65 1.70e+01 d.15.7.1 79134 3gsnB 243 1.71e+01 1f13A 731 1.71e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1bxvA 91 1.75e+01 1aac b.6.1.1 22875 1evuA 731 1.76e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 2p1gA 249 1.78e+01 2vdfA 253 1.78e+01 f.4.4.2 152991 1h2xA 710 1.78e+01 b.69.7.1,c.69.1.4 76598,76599 3lm8A 222 1.81e+01 1ev0A 58 1.85e+01 1ev0A d.71.1.1 39594 1lqbC 162 1.85e+01 b.3.3.1 74186 1qr4B 186 1.88e+01 1qr4B b.1.2.1,b.1.2.1 21988,21989 1s1dA 331 1.91e+01 b.67.3.1 98344 3gm8A 801 1.95e+01 1yllA 200 1.95e+01 b.82.1.17 123653 3d85D 306 1.95e+01 b.1.1.4,b.1.2.1,b.1.2.1 157439,157440,157441 3m5rA 133 1.96e+01 3fwmA 751 1.98e+01 2imjA 166 1.99e+01 d.17.4.23 147725 3k6oA 224 2.00e+01 1y4wA 518 2.02e+01 b.29.1.19,b.67.2.3 116470,116471 1ioaA 240 2.03e+01 1led b.29.1.1 24168 1lm8V 160 2.04e+01 b.3.3.1 74035 1of5B 184 2.04e+01 d.17.4.2 86934 2cclA 158 2.05e+01 b.2.2.2 130248 1rj8A 164 2.06e+01 b.22.1.1 97547 1upqA 123 2.07e+01 b.55.1.1 113392 1k24A 253 2.08e+01 f.4.4.2 72002 1stfI 98 2.10e+01 1stfI d.17.1.2 38006 2cirA 297 2.12e+01 2cwzA 141 2.13e+01 d.38.1.7 130961 3hr6A 436 2.15e+01 1ybyA 215 2.15e+01 1ex0A 731 2.16e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 3l60A 250 2.16e+01 1rhfA 182 2.21e+01 b.1.1.1,b.1.1.4 97469,97470 3ii7A 306 2.25e+01 2k5tA 128 2.26e+01 2iqyA 190 2.27e+01 2aexA 346 2.30e+01 1vcbC 160 2.34e+01 1vcbC b.3.3.1 22535 3cmgA 667 2.39e+01 2wkpA 332 2.39e+01 1rg9A 383 2.46e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1lf2A 331 2.51e+01 b.50.1.2 77914 1sr4C 166 2.51e+01 b.42.2.1 105950 3kf8A 220 2.54e+01 3fe4A 278 2.57e+01 2woyA 356 2.61e+01 1zbmA 280 2.63e+01 c.94.1.1 124858 1lpjA 133 2.63e+01 b.60.1.2 78123 2fhqA 141 2.68e+01 b.45.1.1 133497 1aohA 147 2.68e+01 1aohA b.2.2.2 22401 1qhoA 686 2.71e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 3cnvA 162 2.71e+01 d.190.1.2 156844 2kkzA 140 2.76e+01 3hf5A 116 2.77e+01 2rhkA 140 2.81e+01 1mv3A 213 2.81e+01 b.34.2.1 91468 1vr4A 103 2.88e+01 d.230.5.1 120432 1id2A 106 2.91e+01 1aac b.6.1.1 62288 3cbtA 237 2.94e+01 1jq4A 98 2.97e+01 d.15.4.2 67083 1pm4A 119 3.00e+01 b.135.1.1 94891 3lh5A 251 3.03e+01 2eixA 243 3.04e+01 3fceA 512 3.07e+01 2w2aA 194 3.07e+01 3exmA 237 3.10e+01 3gkeA 349 3.11e+01 2qr5A 582 3.15e+01 b.69.7.2,c.69.1.33 151278,151279 2pa7A 141 3.16e+01 b.82.1.1 149339 1fieA 731 3.20e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 3brnA 157 3.21e+01 3kl7A 235 3.25e+01 3hzpA 131 3.32e+01 2ichA 335 3.35e+01 b.176.1.1 147602 2wnkA 238 3.37e+01 1bw8A 321 3.40e+01 1bw8A b.2.7.1 22482 3fm0A 345 3.42e+01 1mkeA 152 3.42e+01 b.55.1.4 79231 2wkrA 332 3.44e+01 3elqA 571 3.45e+01 1cc3A 130 3.47e+01 1nwpA b.6.1.1 23008 1dzoA 123 3.48e+01 1dzoA d.24.1.1 38378 3bqwA 351 3.49e+01 3ibmA 167 3.50e+01 3cjxA 165 3.50e+01 2pltA 98 3.51e+01 b.6.1.1 22862 1vl7A 157 3.52e+01 b.45.1.1 108732 1xxgA 233 3.55e+01 3lycA 241 3.56e+01 1j2zA 270 3.61e+01 b.81.1.1 90805 2vh1A 220 3.61e+01 3pcgM 238 3.62e+01 3pchM b.3.6.1 22742 1wduA 245 3.69e+01 d.151.1.1 109286 1qr4A 186 3.73e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 2oz4A 265 3.74e+01 b.1.1.3,b.1.1.4,b.1.1.4 149099,149100,149101 3gzuC 397 3.74e+01 2j73A 103 3.76e+01 b.3.1.3 147899 3dqgA 151 3.77e+01 1y89A 238 3.79e+01 3e0fA 301 3.80e+01 2wzaA 374 3.86e+01 1o4tA 133 3.86e+01 b.82.1.9 86622 1im3D 95 3.87e+01 1im3D b.1.18.5 62568 1utyA 187 3.87e+01 b.147.1.1 108036 3fx6A 307 3.87e+01 1gq8A 319 3.87e+01 b.80.1.5 70350 3cihA 739 3.88e+01 2gc9A 179 3.89e+01 b.60.1.6 134972 1azrA 128 3.92e+01 1nwpA b.6.1.1 22983 1qhdA 398 3.93e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 3fsnA 533 3.94e+01 1g4mA 393 3.95e+01 b.1.18.11,b.1.18.11 65143,65144 2hxdA 204 3.95e+01 3lqwA 163 3.97e+01 2furA 209 4.00e+01 b.45.1.1 134185 1qjpA 171 4.02e+01 1bxwA f.4.1.1 43742 1yoxA 250 4.03e+01 b.82.5.2 123789 2zhnA 148 4.06e+01 2yv8A 164 4.07e+01 3kdhA 190 4.07e+01 3hn3A 613 4.09e+01 2ft6A 124 4.09e+01 2vqeE 162 4.13e+01 i.1.1.3 153429 2pz4A 239 4.15e+01 1v10A 521 4.19e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2hu5A 582 4.19e+01 b.69.7.2,c.69.1.33 136763,136764 3cox 507 4.19e+01 1b8sA 3coxA 507 4.19e+01 c.3.1.2,d.16.1.1 30332,37863 3g3sA 249 4.19e+01 3acpA 417 4.24e+01 2qy1A 330 4.26e+01 3gdcA 288 4.27e+01 2c46A 241 4.33e+01 3fkuA 338 4.35e+01 1ln1A 214 4.35e+01 d.129.3.2 74038 1hg8A 349 4.38e+01 b.80.1.3 65830 3i4qA 176 4.41e+01 1kwfA 363 4.41e+01 a.102.1.2 73078 2zxeB 305 4.44e+01 1v4aA 440 4.45e+01 a.24.16.4,d.218.1.9 108350,108351 1bxxA 285 4.50e+01 1bw8A b.2.7.1 22483 3i98A 178 4.52e+01 2ozhA 142 4.53e+01 1p0yA 444 4.54e+01 a.166.1.1,b.85.7.3 87654,87655 1gpiA 431 4.55e+01 b.29.1.10 65450 3d1mC 102 4.55e+01 2z06A 252 4.60e+01 d.159.1.10 153906 2wkqA 332 4.61e+01 2azaA 129 4.64e+01 1nwpA b.6.1.1 22901 3m07A 618 4.65e+01 2gx9A 129 4.68e+01 d.299.1.1 135828 1wyxA 69 4.68e+01 1x6zA 123 4.68e+01 d.24.1.1 121763 2gllA 171 4.69e+01 3lg2A 292 4.69e+01 1ojqA 212 4.70e+01 d.166.1.1 93146 1jt8A 102 4.70e+01 b.40.4.5 63279 1jv2A 957 4.71e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 2uubE 162 4.72e+01 d.14.1.1,d.50.1.2 139936,139937 2g5gX 268 4.73e+01 c.150.1.1 147084 2iwkA 642 4.73e+01 3c8xA 206 4.73e+01 2wx6A 388 4.74e+01 1m4lA 307 4.74e+01 c.56.5.1 78604 2ccwA 129 4.77e+01 b.6.1.1 130259 3ks9A 496 4.78e+01 2oszA 93 4.79e+01 1w8oA 601 4.81e+01 b.1.18.2,b.18.1.1,b.68.1.1 114374,114375,114376 3g0bA 740 4.84e+01 1z02A 446 4.86e+01 2octA 98 4.88e+01 2w68A 195 4.90e+01 1a4aA 129 4.92e+01 1nwpA b.6.1.1 22907 1q0xH 221 4.97e+01 b.1.1.1,b.1.1.2 95517,95518 1jzgA 128 4.99e+01 b.6.1.1 67855 2pamA 141 5.02e+01 b.82.1.1 149348 1cb8A 678 5.05e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1p4qA 52 5.07e+01 j.96.1.1 87777 1bb9 115 5.09e+01 1bb9 1bb9A 115 5.09e+01 b.34.2.1 24554 3lwxA 199 5.10e+01 1u00A 227 5.11e+01 a.8.4.1,b.130.1.1 112900,112901 1eut 605 5.17e+01 1eut 3bghA 236 5.21e+01 2uxtA 451 5.24e+01 1icxA 155 5.25e+01 d.129.3.1 71191 2ntxA 365 5.28e+01 3bwuD 125 5.30e+01 b.167.1.1 155701 1hfuA 503 5.37e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1aznA 128 5.38e+01 1nwpA b.6.1.1 23003 3fpxA 499 5.40e+01 3f3kA 265 5.41e+01 1ag0A 129 5.45e+01 1nwpA b.6.1.1 23001 1cuoA 129 5.46e+01 1nwpA b.6.1.1 23015 1zkiA 133 5.46e+01 d.38.1.5 125199 1ebdA 455 5.47e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1j1lA 290 5.50e+01 b.82.1.12 90766 1azcA 129 5.52e+01 1nwpA b.6.1.1 22899 1rm8A 169 5.53e+01 d.92.1.11 97660 2pp6A 102 5.54e+01 b.106.1.2 149728 3gc3A 385 5.56e+01 1qhqA 140 5.61e+01 1qhqA b.6.1.1 63326 2go8A 122 5.62e+01 d.58.4.5 147144 1ddwA 120 5.63e+01 1evhA b.55.1.4 27001 2ctc 307 5.63e+01 1aye 1kit 757 5.63e+01 1kit 1xdfA 157 5.63e+01 d.129.3.1 121868 1wcqA 601 5.65e+01 b.1.18.2,b.18.1.1,b.68.1.1 120894,120895,120896 2wd6A 349 5.66e+01 2wtmA 251 5.67e+01 1a0tP 413 5.67e+01 1a0tP f.4.3.2 43794 3fnbA 405 5.68e+01 1tvfA 369 5.69e+01 b.105.1.2,e.3.1.1 107358,107359 3f1tA 148 5.70e+01 3dmcA 134 5.71e+01 d.17.4.10 157805 1wyzA 242 5.77e+01 c.90.1.1 121471 3lh9A 340 5.78e+01 1xl4A 301 5.79e+01 b.1.18.16,f.14.1.1 115430,115431 1xeuA 263 5.79e+01 1prn 289 5.80e+01 3prn 1i31A 314 5.82e+01 1bw8A b.2.7.1 22481 1w0pA 781 5.89e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1clc 639 5.91e+01 1clc 1clcA 639 5.91e+01 a.102.1.2,b.1.18.2 18835,21872 3d7iA 105 5.92e+01 3cpnA 330 5.93e+01 2vn4A 599 5.93e+01 3ft0A 129 5.93e+01 1r0uA 148 6.00e+01 b.60.1.5 96741 3kg9A 296 6.02e+01 2hlvA 160 6.03e+01 2wvxA 744 6.07e+01 1ddvA 111 6.09e+01 1evhA b.55.1.4 27002 1a65A 504 6.09e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1qj8A 148 6.12e+01 1qj8A f.4.1.1 43744 3bqoA 211 6.20e+01 a.146.1.1 155503 3gneA 252 6.22e+01 2fexA 188 6.27e+01 c.23.16.2 133354 3f7pC 248 6.36e+01 3ld7A 101 6.37e+01 2kdgA 100 6.37e+01 1y1nA 291 6.39e+01 2axtZ 62 6.40e+01 f.17.5.1 144941 3divA 499 6.41e+01 3gbmA 334 6.41e+01 2nsqA 155 6.44e+01 1yduA 170 6.44e+01 b.162.1.1 123003 3bjnA 165 6.46e+01 3kz4C 397 6.48e+01 1pmhX 185 6.49e+01 b.18.1.18 104193 1sluA 142 6.49e+01 1sluA b.16.1.1 23685 2ii1A 301 6.55e+01 2gysA 419 6.65e+01 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 7ahlA 293 6.65e+01 7ahlA f.6.1.1 43812 3fswA 128 6.70e+01 2vqaA 361 6.70e+01 2c30A 321 6.72e+01 2ausA 334 6.74e+01 1suwA 249 6.90e+01 e.52.1.1 106027 3heiA 174 6.95e+01 1fnmA 691 6.95e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 2gufA 594 7.00e+01 f.4.3.3 135736 1ntvA 152 7.01e+01 b.55.1.2 86168 2ealA 148 7.02e+01 1y07A 128 7.07e+01 3g4eA 297 7.10e+01 2hzqA 174 7.10e+01 2gmnA 274 7.11e+01 d.157.1.1 147132 3i9hA 88 7.13e+01 1h9dB 134 7.19e+01 2jhbA b.54.1.1 60822 1bxeA 113 7.23e+01 1bxeA d.55.1.1 38898 1qx4A 274 7.29e+01 b.43.4.2,c.25.1.1 104624,104625 3bwsA 433 7.30e+01 3hacA 728 7.34e+01 2x10A 545 7.34e+01 1iow 306 7.35e+01 1iow 1iowA 306 7.35e+01 c.30.1.2,d.142.1.1 31713,41481 3lywA 90 7.41e+01 1tyeB 440 7.41e+01 b.1.15.1,c.62.1.1,g.16.2.1 112830,112831,112832 3bz1Z 62 7.52e+01 2kppA 114 7.54e+01 1r9cA 139 7.56e+01 d.32.1.2 97255 3hrzD 741 7.61e+01 1o4yA 288 7.63e+01 b.29.1.2 92473 3bypA 94 7.65e+01 d.52.9.1 155726 1ifrA 121 7.65e+01 b.1.16.1 71203 1fjgE 162 7.65e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1qtnB 95 7.71e+01 1pauB 3ddvA 145 7.74e+01 d.190.1.2 157563 2we0A 286 7.76e+01 3jv1A 182 7.77e+01 2q86A 229 7.83e+01 1avbA 226 7.93e+01 1led b.29.1.1 24158 3k1uA 330 7.95e+01 1l0iA 78 7.96e+01 a.28.1.1 77643 1f3uB 171 7.97e+01 1f3uB b.65.1.1 27525 3g5cA 510 7.98e+01 1vlrA 350 8.00e+01 d.13.1.3,d.246.1.1 108860,108861 2wiqA 257 8.00e+01