# 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.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 1pjcA 361 7.57e-01 1sayA c.2.1.4,c.23.12.2 30101,31361 1pjbA 361 8.54e-01 1sayA c.2.1.4,c.23.12.2 30103,31363 1sayA 361 1.13e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 1ouwA 152 2.01e+00 b.77.3.1 93571 1qb5D 99 3.65e+00 b.40.2.1 88357 1a73A 163 4.46e+00 1a73A d.4.1.3 37145 1yfqA 342 4.52e+00 1evxA 162 5.19e+00 1a73A d.4.1.3 37149 1y89A 238 7.46e+00 1e9rA 437 7.88e+00 c.37.1.11 64827 1q0uA 219 8.18e+00 c.37.1.19 95512 1k4mA 213 8.99e+00 c.26.1.3 77258 1f0iA 504 9.73e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1fjgP 88 1.02e+01 1emwA d.27.1.1 38444 1d6zA 727 1.08e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1tc5A 194 1.12e+01 c.110.1.1 106752 1fx3A 169 1.13e+01 1fx3B d.33.1.1 38524 1yal 218 1.24e+01 1cs8A d.3.1.1 37025 2cuaA 135 1.24e+01 2cuaA b.6.1.2 23039 1v0wA 506 1.25e+01 d.136.1.2,d.136.1.2 108220,108221 1u4cA 349 1.35e+01 b.69.4.2 107666 1a48 306 1.41e+01 1a48 d.143.1.1 41590 1ejbA 168 1.46e+01 1rvv1 c.16.1.1 59417 1tiiD 99 1.47e+01 1tiiD b.40.2.1 24965 1j3bA 529 1.47e+01 c.91.1.1,c.109.1.1 77071,77072 1v5eA 590 1.55e+01 1ykfA 352 1.66e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1klo 162 1.67e+01 1klo g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 1oacA 727 1.71e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 2ag9A 164 1.75e+01 1nhcA 336 1.77e+01 b.80.1.3 91879 1obdA 306 1.78e+01 d.143.1.1 86767 1pk6C 129 1.78e+01 b.22.1.1 94803 1rl6A 177 1.83e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 2ag4A 164 2.03e+01 1cc1S 283 2.06e+01 2frvA e.19.1.1 43313 1o8uA 257 2.11e+01 c.14.1.3 81194 1oaoA 674 2.14e+01 e.26.1.2 86744 2cnqA 306 2.16e+01 1eyyA 510 2.17e+01 1eyyA c.82.1.1 35389 1pu5A 164 2.18e+01 b.95.1.1 104310 1szoA 257 2.25e+01 c.14.1.3 106164 1vdwA 254 2.25e+01 e.7.1.1 100569 1ehkB 168 2.29e+01 2cuaA b.6.1.2,f.17.2.1 23041,43625 1i24A 404 2.30e+01 c.2.1.2 83663 1rxyA 253 2.41e+01 c.56.2.1 98065 1ydgA 211 2.46e+01 1lx7A 253 2.46e+01 c.56.2.1 74329 1qrrA 394 2.46e+01 1qrrA c.2.1.2 29824 2fox 138 2.66e+01 5nul c.23.5.1 31197 1mkyA 439 2.69e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2ch8A 201 2.74e+01 2fliA 220 2.78e+01 1o66A 275 2.80e+01 c.1.12.8 92547 1b7bA 310 2.82e+01 1b7bA c.73.1.1 34963 2b81A 323 2.93e+01 1ejeA 192 3.00e+01 1ejeA b.45.1.2 25757 1vq2A 193 3.20e+01 1lxa 262 3.38e+01 1lxa b.81.1.1 28052 3ullA 132 3.40e+01 3ullA b.40.4.3 25282 1s62A 106 3.44e+01 1lxjA 104 3.60e+01 d.58.48.1 84736 1fwyA 331 3.61e+01 1fwyA b.81.1.4,c.68.1.5 28064,34522 1ww9A 392 3.62e+01 2bryA 497 3.67e+01 1fxjA 331 3.73e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1nal3 297 3.75e+01 1nal3 2aq9A 262 3.80e+01 1gdeA 389 3.80e+01 c.67.1.1 60456 1uohA 226 3.82e+01 d.211.1.1 99690 1r6vA 671 3.92e+01 1gd9A 389 3.98e+01 c.67.1.1 60454 1fx3B 169 4.01e+01 1fx3B d.33.1.1 38525 1iuhA 198 4.06e+01 d.61.1.2 83711 1xt5A 135 4.11e+01 1vajA 214 4.20e+01 1td4A 115 4.23e+01 2b4lA 268 4.24e+01 2ew8A 249 4.24e+01 1hkfA 122 4.24e+01 b.1.1.1 83553 1ws0A 156 4.32e+01 1nmuB 104 4.36e+01 d.79.3.1 80666 2cxcA 144 4.39e+01 2cxhA 217 4.40e+01 1jqlB 140 4.57e+01 c.37.1.20 63234 1hl2A 297 4.57e+01 c.1.10.1 83581 1hv9A 456 4.61e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1ha3A 405 4.63e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1ez0A 510 4.66e+01 1eyyA c.82.1.1 35385 3ladA 476 4.67e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1o97C 264 4.69e+01 c.26.2.3 81232 1hqkA 154 4.76e+01 c.16.1.1 65902 1x1gA 129 4.90e+01 1spuB 727 4.90e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1zesA 125 4.95e+01 1wxcA 281 4.96e+01 1xkiA 162 5.01e+01 2f71A 298 5.06e+01 1efuA 385 5.13e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1rhi3 236 5.17e+01 1aym3 1czfA 362 5.19e+01 1czfA b.80.1.3 28031 1ojxA 263 5.20e+01 c.1.10.1 93164 1hynP 379 5.28e+01 1hynP d.112.1.2 61408 1t8xA 267 5.28e+01 1zckA 154 5.30e+01 2b3yA 888 5.30e+01 2bzlA 325 5.33e+01 1krhA 338 5.39e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1exmA 405 5.44e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1gq6A 313 5.45e+01 c.42.1.1 70341 2cg4A 152 5.63e+01 1hup 141 5.67e+01 1rtm1 d.169.1.1,h.1.1.1 42354,45422 1ujpA 271 5.73e+01 c.1.2.4 99462 1yreA 197 5.75e+01 1xbsA 149 5.83e+01 2etgA 296 5.91e+01 1ns5A 155 5.92e+01 c.116.1.3 80705 1w8sA 263 5.93e+01 1rxdA 159 5.99e+01 2cu1A 103 6.26e+01 1w7lA 422 6.32e+01 c.67.1.1 109226 1kewA 361 6.37e+01 c.2.1.2 68544 1ebdA 455 6.43e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1so9A 164 6.44e+01 b.146.1.1 105842 1s7hA 200 6.51e+01 d.58.48.2 105349 1vhvA 268 6.53e+01 c.90.1.1 100704 1jr3D 343 6.58e+01 a.80.1.1,c.37.1.20 63251,63252 2fkkA 206 6.62e+01 1tzaA 134 6.71e+01 b.1.23.1 107468 1w85A 368 6.71e+01 2es9A 115 6.88e+01 1sh8A 154 6.88e+01 d.38.1.5 105549 1fonA 240 6.95e+01 5ptp b.47.1.2 26231 1h1yA 228 7.16e+01 c.1.2.2 76506 1h7zA 194 7.20e+01 1qhvA b.21.1.1 60733 1e12A 253 7.24e+01 1c3wA f.13.1.1 43428 2cz2A 223 7.32e+01 1nal1 297 7.40e+01 1nal3 1ew3A 159 7.46e+01 1mup b.60.1.1 27114 1h3nA 878 7.50e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1c3kA 147 7.57e+01 1jotA b.77.3.1 27984 1kzhA 555 7.59e+01 c.89.1.1 73361 1bylA 125 7.60e+01 1bylA d.32.1.2 38495 1c96A 753 7.66e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1ob8A 135 7.67e+01 1b34A 119 7.71e+01 1d3bA b.38.1.1 24796 1k75A 434 7.71e+01 c.82.1.2 68253 1g13A 162 7.72e+01 1g13A b.95.1.1 60194 1rz1A 161 7.77e+01 b.45.1.2 98124 1k3fA 253 7.88e+01 c.56.2.1 68105 1kaeA 434 7.91e+01 c.82.1.2 72247 7reqB 637 7.99e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1kq3A 376 8.00e+01 e.22.1.2 68790 1h2cA 140 8.11e+01 b.31.1.1 83462 1jzuA 157 8.32e+01 b.60.1.1 84271 1gkxA 388 8.33e+01 a.29.5.1,d.122.1.4 65266,65267 1t9bA 677 8.36e+01 1vclA 432 8.40e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1l9mA 692 8.46e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1fmcA 255 8.48e+01 1cydA c.2.1.2 29856 1zhaA 267 8.50e+01 2fsp 124 8.57e+01 1dz3A c.23.1.1 31119 1g8oA 310 8.65e+01 1g8oA c.68.1.9 60375 2bl1A 172 8.65e+01 1thqA 170 8.66e+01 f.4.1.2 106920 1emwA 88 8.66e+01 1emwA d.27.1.1 38448 7acn 754 8.72e+01 1amj c.8.2.1,c.83.1.1 30717,35393 2c07A 285 8.74e+01 1aax 321 8.91e+01 1pty c.45.1.2 32657 1dghB 498 8.95e+01 1cf9A e.5.1.1 42791