# List of top-scoring protein chains for t2k-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.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 2.51e-02 2i5vO 251 9.26e-02 2c9oA 456 3.13e-01 2v8pA 271 7.11e-01 2hkdA 320 1.04e+00 1ospO 257 1.30e+00 1ospO b.76.1.1 27971 1h6fA 193 1.36e+00 b.2.5.4 70901 2aexA 346 1.39e+00 2g8cO 251 1.57e+00 2oy7A 320 1.69e+00 1d7pM 159 2.64e+00 1cztA b.18.1.2 23718 1b78A 193 2.66e+00 1b78A c.51.4.1 33221 1bxeA 113 2.82e+00 1bxeA d.55.1.1 38898 2dtcA 126 2.84e+00 2d7vA 162 3.14e+00 d.227.1.1 146468 1h7zA 194 3.21e+00 1qhvA b.21.1.1 60733 2cg4A 152 3.88e+00 a.4.5.32,d.58.4.2 130417,130418 1evuA 731 4.66e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 3lh5A 251 4.85e+00 1icxA 155 5.06e+00 d.129.3.1 71191 3fhhA 640 5.75e+00 3hnyM 159 5.86e+00 1k55A 246 6.90e+00 e.3.1.1 68156 1bquA 215 7.30e+00 1bquA b.1.2.1,b.1.2.1 22066,22067 1v0eA 666 8.07e+00 b.68.1.2,b.108.1.3 113466,113467 1btl 263 8.47e+00 1btl 2z4iA 233 8.88e+00 1i4jA 110 9.88e+00 d.55.1.1 76734 1nziA 159 1.01e+01 b.23.1.1,g.3.11.1 86449,86450 1sb2A 133 1.07e+01 d.169.1.1 118927 2ntxA 365 1.08e+01 1mhxA 65 1.14e+01 d.15.7.1 79134 3exmA 237 1.16e+01 2z14A 133 1.16e+01 1kb0A 677 1.18e+01 a.3.1.6,b.70.1.1 68378,68379 1xzzA 246 1.21e+01 1m40A 263 1.21e+01 e.3.1.1 74437 1ifrA 121 1.35e+01 b.1.16.1 71203 2q9kA 151 1.37e+01 1fofA 246 1.45e+01 1fofA e.3.1.1 42763 1wduA 245 1.46e+01 d.151.1.1 109286 1ex0A 731 1.48e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2zwaA 695 1.50e+01 3k63A 126 1.53e+01 1lpjA 133 1.56e+01 b.60.1.2 78123 2pltA 98 1.59e+01 b.6.1.1 22862 1k55C 246 1.59e+01 e.3.1.1 68158 2vzpA 127 1.60e+01 2asbA 251 1.60e+01 b.40.4.5,d.52.3.1,d.52.3.1 127244,127245,127246 3ginA 160 1.61e+01 2qtdA 105 1.64e+01 3gvkA 670 1.69e+01 2zw3A 226 1.72e+01 2klaA 106 1.78e+01 1j5wA 298 1.84e+01 d.104.1.1 71589 3ju4A 670 1.84e+01 1wfwA 74 1.85e+01 b.34.2.1 114595 1u00A 227 1.97e+01 a.8.4.1,b.130.1.1 112900,112901 1a65A 504 1.99e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1k0rA 366 2.00e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1of5B 184 2.00e+01 d.17.4.2 86934 1k4fA 248 2.02e+01 e.3.1.1 68138 3cbtA 237 2.02e+01 1ee9A 320 2.05e+01 1ee9A c.2.1.7,c.58.1.2 30288,33936 1sh8A 154 2.06e+01 d.38.1.5 105549 2wxuA 370 2.09e+01 1p4uA 153 2.11e+01 b.1.10.2 87780 2vh4A 381 2.29e+01 2k5tA 128 2.31e+01 3f7eA 131 2.32e+01 1im3D 95 2.33e+01 1im3D b.1.18.5 62568 1epaA 164 2.36e+01 1epaA b.60.1.1 27128 1yqyA 523 2.38e+01 d.92.1.14,d.166.1.1 123903,123904 2pefA 373 2.42e+01 2v0uA 146 2.44e+01 1f13A 731 2.47e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 2j2jA 197 2.50e+01 b.21.1.1 147852 2imjA 166 2.53e+01 d.17.4.23 147725 1axj 122 2.60e+01 1axj 1xeuA 263 2.60e+01 3cslA 865 2.63e+01 1l0iA 78 2.67e+01 a.28.1.1 77643 3gvjA 670 2.69e+01 2calA 154 2.71e+01 1h6lA 353 2.72e+01 b.68.3.1 60687 3dzmA 214 2.73e+01 3drnA 161 2.79e+01 1ca1 370 2.81e+01 1ca1 1ca1A 370 2.81e+01 a.124.1.1,b.12.1.3 19340,23648 1t8kA 77 2.86e+01 a.28.1.1 106666 1lqbC 162 2.87e+01 b.3.3.1 74186 3gcb 470 2.89e+01 3gcb 3gcbA 470 2.89e+01 d.3.1.1 37032 2iumA 248 2.91e+01 1a0tP 413 2.96e+01 1a0tP f.4.3.2 43794 3heiA 174 2.96e+01 3dqgA 151 3.03e+01 2dyiA 162 3.04e+01 3e8pA 164 3.06e+01 3fceA 512 3.10e+01 2vdfA 253 3.11e+01 f.4.4.2 152991 1hfuA 503 3.13e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 2octA 98 3.21e+01 2it1A 362 3.21e+01 2e01A 457 3.22e+01 3k6oA 224 3.24e+01 1x6zA 123 3.25e+01 d.24.1.1 121763 1kit 757 3.27e+01 1kit 1qlgA 355 3.29e+01 1qlgA b.68.3.1 27627 2nnuA 205 3.31e+01 b.91.1.1 138401 2wkrA 332 3.32e+01 1ur5A 309 3.32e+01 c.2.1.5,d.162.1.1 99807,99808 3i1iA 377 3.36e+01 1t4wA 196 3.39e+01 b.2.5.2 106427 3cxbA 336 3.42e+01 1fqgA 263 3.48e+01 1btl e.3.1.1 42699 2w7vA 95 3.48e+01 1o0wA 252 3.50e+01 a.149.1.1,d.50.1.1 80751,80752 1khoA 370 3.50e+01 a.124.1.1,b.12.1.3 72489,72490 1bj7 156 3.52e+01 1bj7 1bj7A 156 3.52e+01 b.60.1.1 27113 1vcbC 160 3.53e+01 1vcbC b.3.3.1 22535 1yp1A 202 3.60e+01 3jxsA 174 3.77e+01 1fieA 731 3.78e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 2p5iA 288 3.79e+01 d.104.1.3 149248 3b4wA 495 3.80e+01 2hh6A 113 3.83e+01 a.69.4.1 147285 2wjhA 166 3.84e+01 2igtA 332 3.86e+01 c.66.1.51 137401 1azrA 128 3.86e+01 1nwpA b.6.1.1 22983 1id2A 106 3.88e+01 1aac b.6.1.1 62288 1jwoA 97 3.94e+01 d.93.1.1 63310 1b8mA 119 3.97e+01 1bndA g.17.1.3 44797 2qimA 158 4.15e+01 1h0pA 182 4.16e+01 b.62.1.1 76450 2vnlA 151 4.23e+01 2uxtA 451 4.27e+01 2dpkA 152 4.28e+01 b.1.27.1 131616 2v4iA 173 4.29e+01 2ogrA 229 4.32e+01 1zvfA 176 4.36e+01 b.82.1.20 146029 2c36A 285 4.38e+01 1qydA 313 4.44e+01 c.2.1.2 96583 2e8dA 22 4.51e+01 2gopA 347 4.57e+01 2bs9A 503 4.63e+01 b.71.1.2,c.1.8.3 129062,129063 1dzoA 123 4.63e+01 1dzoA d.24.1.1 38378 1xrtA 467 4.64e+01 b.92.1.3,c.1.9.6 122258,122259 1lnsA 763 4.66e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1x1iA 752 4.66e+01 a.102.3.2,b.24.1.1,b.30.5.2 121584,121585,121586 1lktA 104 4.69e+01 1lktA b.90.1.1 28398 1lrwA 600 4.70e+01 b.70.1.1 91111 1nwpA 128 4.70e+01 1nwpA b.6.1.1 23011 1wu4A 396 4.73e+01 a.102.1.2 121272 1upqA 123 4.74e+01 b.55.1.1 113392 3dhvA 512 4.74e+01 3itaA 352 4.76e+01 2vzkA 173 4.80e+01 1ermA 263 4.84e+01 1btl e.3.1.1 42690 3pcgM 238 4.88e+01 3pchM b.3.6.1 22742 3bwuD 125 4.92e+01 b.167.1.1 155701 3hzpA 131 4.93e+01 3b7yA 153 4.94e+01 3fw8A 495 5.01e+01 1h9dB 134 5.03e+01 2jhbA b.54.1.1 60822 2htiA 185 5.07e+01 b.45.1.1 136744 1k24A 253 5.07e+01 f.4.4.2 72002 1edzA 320 5.08e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 2gufA 594 5.13e+01 f.4.3.3 135736 3a2sX 355 5.19e+01 1vl7A 157 5.20e+01 b.45.1.1 108732 1zx5A 300 5.23e+01 b.82.1.3 125763 1he7A 126 5.24e+01 1wwcA b.1.1.4 60970 1w0pA 781 5.28e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 3fw9A 495 5.29e+01 2bwqA 129 5.31e+01 b.7.1.2 129380 2v8qA 157 5.33e+01 d.129.6.2 152781 1bavA 309 5.35e+01 1aye c.56.5.1 33806 1sa3A 262 5.37e+01 c.52.1.23 105400 1jb7A 495 5.39e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 3jtzA 88 5.40e+01 1p0zA 131 5.48e+01 d.110.6.1 93882 1gcb 454 5.51e+01 3gcb 1c3hA 137 5.51e+01 b.22.1.1 90405 3cseA 227 5.51e+01 2r2yA 153 5.51e+01 2ggvA 56 5.60e+01 1jmaA 290 5.62e+01 b.1.1.1 63177 2a2jA 246 5.72e+01 b.45.1.1 126033 2wb7A 526 5.74e+01 1ut7A 171 5.75e+01 b.143.1.1 99906 1um8A 376 5.75e+01 c.37.1.20 99580 3cihA 739 5.77e+01 3brzA 439 5.80e+01 1ojqA 212 5.86e+01 d.166.1.1 93146 3l60A 250 5.89e+01 3fwaA 497 5.90e+01 1gmiA 136 5.93e+01 b.7.1.1 65309 1lm8V 160 5.95e+01 b.3.3.1 74035 3fw7A 498 5.99e+01 1dnlA 199 6.01e+01 1ci0A b.45.1.1 25753 2cwzA 141 6.02e+01 d.38.1.7 130961 3kfvA 308 6.05e+01 3d2hA 538 6.13e+01 1ze3D 125 6.13e+01 b.167.1.1 124976 1qjpA 171 6.16e+01 1bxwA f.4.1.1 43742 1agdB 99 6.20e+01 1agdB b.1.1.2 20742 1k5nB 100 6.21e+01 b.1.1.2 77268 3cjxA 165 6.23e+01 2wnkA 238 6.23e+01 2w68A 195 6.24e+01 2cjtA 131 6.26e+01 b.7.1.1 130549 3bf2A 152 6.31e+01 2dr3A 247 6.34e+01 1ly7A 121 6.35e+01 d.82.2.1 74339 1uxjA 309 6.44e+01 c.2.1.5,d.162.1.1 108112,108113 1vr4A 103 6.49e+01 d.230.5.1 120432 1i71A 83 6.52e+01 5hpgA g.14.1.1 61864 3hdjA 313 6.54e+01 3hwoA 394 6.57e+01 2hb0A 369 6.68e+01 2zxeB 305 6.69e+01 1qtnB 95 6.69e+01 1pauB 3kf8A 220 6.71e+01 2jx5A 69 6.74e+01 1tr8A 102 6.74e+01 1ebdA 455 6.75e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1kwfA 363 6.80e+01 a.102.1.2 73078 1cem 363 6.82e+01 1cem 1v1qA 134 6.83e+01 b.40.4.3 113490 3bqoA 211 6.86e+01 a.146.1.1 155503 2kieA 124 6.92e+01 3bs0A 439 6.93e+01 3gsyA 519 6.95e+01 2pooA 355 6.96e+01 1qlgA b.68.3.1 27626 2z06A 252 6.98e+01 d.159.1.10 153906 3aagA 291 7.00e+01 1xnaA 183 7.06e+01 1xnaA b.18.1.8 23773 2fkkA 206 7.12e+01 2qgoA 141 7.20e+01 3d7iA 105 7.35e+01 1dleA 298 7.38e+01 1dleA b.47.1.2 26312 2ft6A 124 7.38e+01 1fohA 664 7.38e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 2ctc 307 7.47e+01 1aye 3k26A 366 7.54e+01 3kkfA 105 7.65e+01 2oszA 93 7.66e+01 1w7jA 795 7.67e+01 b.34.3.1,c.37.1.9 120688,120689 3fx6A 307 7.69e+01 3bz1Z 62 7.73e+01 1vprA 374 7.73e+01 b.60.1.7 120066 2p49B 123 7.73e+01 b.1.1.1 149207 2vnuD 760 7.81e+01 b.40.4.5,b.40.4.5,b.40.4.5,b.40.4.16 153344,153345,153346,153347 3hxkA 276 7.85e+01 1ybhA 590 7.85e+01 c.31.1.3,c.36.1.5,c.36.1.9 122891,122892,122893 3f1tA 148 7.86e+01 2p45B 123 7.87e+01