# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 2ap1A 327 7.84e-02 1rypA 243 2.20e-01 1pmaA d.153.1.4 41932 1g0uG 252 4.40e-01 d.153.1.4 41952 2ahqA 76 6.46e-01 1yrvA 169 1.20e+00 1wzvA 155 1.26e+00 2b20A 403 1.84e+00 1wxcB 134 1.97e+00 1fseA 74 2.22e+00 1fseA a.4.6.2 60000 1kxoA 184 2.25e+00 b.60.1.1 84475 1xawA 140 2.29e+00 1f1sA 814 3.29e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1q2hA 69 3.99e+00 a.34.4.1 104498 1z8uA 102 4.07e+00 1zd9A 188 4.35e+00 1o7fA 469 4.47e+00 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1xqaA 113 5.15e+00 2g0uA 92 5.25e+00 1emwA 88 5.30e+00 1emwA d.27.1.1 38448 2ddrA 306 5.39e+00 1diwA 441 6.47e+00 1a8d b.29.1.6,b.42.4.2 24264,25609 1osa 148 6.53e+00 1cll a.39.1.5 17300 1d0hA 469 6.85e+00 1a8d b.29.1.6,b.42.4.2 24265,25610 2a19A 175 6.87e+00 3proC 166 6.98e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1bbpA 173 7.06e+00 1bbpA b.60.1.1 27147 1ufiA 64 7.26e+00 a.30.4.1 99336 1wgxA 73 7.53e+00 1xttA 216 8.00e+00 1jsdA 319 8.30e+00 b.19.1.2 63258 1w23A 360 8.35e+00 1y01A 102 8.63e+00 1a8d 452 8.65e+00 1a8d b.29.1.6,b.42.4.2 24262,25607 1v0wA 506 8.93e+00 d.136.1.2,d.136.1.2 108220,108221 1ahr 146 9.81e+00 1cll a.39.1.5 17287 1a8y 367 9.91e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1u7kA 131 1.02e+01 1a3s 160 1.12e+01 1u9aA d.20.1.1 38335 1g9uA 454 1.15e+01 c.10.2.6 65172 1g4yR 148 1.16e+01 1cll a.39.1.5 60252 1u9aA 160 1.18e+01 1u9aA d.20.1.1 38333 2ajrA 331 1.19e+01 1tn4 159 1.20e+01 1ncx a.39.1.5 17248 1jl5A 454 1.20e+01 c.10.2.6 66830 1hp0A 339 1.23e+01 c.70.1.1 65900 1hozA 339 1.26e+01 c.70.1.1 65898 1mhlC 466 1.32e+01 1mhlC 1zmtA 254 1.32e+01 1yx1A 264 1.34e+01 1cxpC 466 1.35e+01 1mhlC 1wpaA 114 1.35e+01 1zvkA 358 1.35e+01 1d2vC 466 1.40e+01 1mhlC 1cll 148 1.46e+01 1cll a.39.1.5 17263 1q02A 52 1.47e+01 a.5.2.1 95490 2gupA 292 1.47e+01 1v54E 109 1.50e+01 a.118.11.1 100326 1sxjE 354 1.54e+01 a.80.1.1,c.37.1.20 106089,106090 1zoyC 140 1.56e+01 1f0iA 504 1.58e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1t6cA 315 1.60e+01 c.55.1.8,c.55.1.8 106558,106559 1pwxA 254 1.61e+01 c.2.1.2 95262 1ggzA 148 1.64e+01 a.39.1.5 70176 1xkpA 246 1.65e+01 1w0bA 102 1.67e+01 a.7.11.1 108985 4bcl 366 1.67e+01 4bcl b.75.1.1 27968 1hfoA 113 1.70e+01 d.80.1.3 61006 1bjwA 382 1.71e+01 1bjwA c.67.1.1 34349 1u2eA 289 1.75e+01 1b5pA 385 1.75e+01 c.67.1.1 90403 3proD 166 1.77e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1wqgA 185 1.79e+01 2occE 109 1.83e+01 2occE a.118.11.1 19224 1um8A 376 1.84e+01 c.37.1.20 99580 3cln 148 1.87e+01 1cll a.39.1.5 17286 1k4nA 192 1.88e+01 d.32.1.5 72059 1sseB 86 1.89e+01 1q1lA 401 1.95e+01 d.258.1.1 95591 1qhbA 596 1.98e+01 1qhbA a.111.1.2 19055 1uzbA 516 2.06e+01 c.82.1.1 100220 2h88C 140 2.08e+01 1lkkA 105 2.10e+01 1lckA d.93.1.1 40412 2bjkA 516 2.13e+01 1ztpA 251 2.22e+01 1z52A 470 2.24e+01 1fzyA 149 2.24e+01 d.20.1.1 65072 1brwA 433 2.25e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1r85A 379 2.31e+01 c.1.8.3 104839 1preA 470 2.31e+01 1preA d.169.1.2,f.8.1.1 42437,43824 2fbwC 141 2.35e+01 1nnwA 252 2.40e+01 d.159.1.5 80674 1up8A 598 2.54e+01 a.111.1.2 99710 1szoA 257 2.55e+01 c.14.1.3 106164 2fjlA 150 2.57e+01 2grrA 161 2.60e+01 1z5yE 149 2.62e+01 2fi9A 128 2.68e+01 1fxtA 149 2.75e+01 d.20.1.1 65055 1k1fA 72 2.76e+01 a.147.1.1 68007 1fgyA 127 2.76e+01 1faoA b.55.1.1 26976 1vcbC 160 2.76e+01 1vcbC b.3.3.1 22535 1yts 278 2.81e+01 1ytw c.45.1.2 32690 2f3yA 148 2.82e+01 1xzzA 246 2.85e+01 2fm9A 215 2.87e+01 2aegA 268 2.89e+01 1dujA 187 2.90e+01 1dujA d.135.1.1 41449 1xsjA 778 2.91e+01 2dgkA 452 2.95e+01 1ywlA 96 3.06e+01 1shfA 59 3.06e+01 1bbzA b.34.2.1 24462 1hizA 379 3.10e+01 c.1.8.3 65841 1pysA 350 3.10e+01 1pysA d.104.1.1 40775 1x3lA 440 3.11e+01 1ytw 306 3.12e+01 1ytw c.45.1.2 32689 1gt91 357 3.19e+01 1vcvA 226 3.20e+01 1yptA 305 3.23e+01 1ytw c.45.1.2 32686 2fulA 178 3.27e+01 1ynuA 473 3.28e+01 1efnA 59 3.29e+01 1bbzA b.34.2.1 24465 1yh6A 179 3.32e+01 1ybxA 143 3.36e+01 2b0tA 738 3.37e+01 1o5oA 221 3.38e+01 c.61.1.1 92509 1ej8A 140 3.41e+01 1qupA b.1.8.1 22300 1zg2A 107 3.50e+01 2pth 193 3.54e+01 2pth c.56.3.1 33793 1eqfA 280 3.55e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1klqA 197 3.56e+01 d.135.1.1 68689 1crl 534 3.59e+01 1thg c.69.1.17 34765 2db9A 149 3.65e+01 1kllA 130 3.66e+01 d.32.1.2 72720 1exrA 148 3.66e+01 1cll a.39.1.5 17299 1lqbC 162 3.68e+01 b.3.3.1 74186 1tf1A 198 3.69e+01 d.110.2.2 106826 1ag8A 499 3.70e+01 1bpwA c.82.1.1 35341 1t1gA 364 3.76e+01 c.41.1.2 106246 1m7yA 435 3.82e+01 c.67.1.4 78761 1xn9A 101 3.84e+01 1ayzA 169 3.84e+01 1u9aA d.20.1.1 38326 1zhxA 438 3.84e+01 1o8uA 257 3.85e+01 c.14.1.3 81194 1nrjA 158 3.85e+01 d.110.4.4 86124 1fzqA 181 3.91e+01 1hurA c.37.1.8 32060 1jn5B 250 3.92e+01 d.17.4.2 66922 2b8iA 77 3.95e+01 1b8gA 429 3.97e+01 1b8gA c.67.1.4 34499 1lyvA 306 4.02e+01 c.45.1.2 74348 2f2hA 773 4.03e+01 1azgB 67 4.04e+01 1bbzA b.34.2.1 24471 1jkgB 250 4.06e+01 d.17.4.2 66796 1jqeA 292 4.08e+01 c.66.1.19 71789 1c4zD 154 4.08e+01 1u9aA d.20.1.1 38331 1top 162 4.12e+01 1ncx a.39.1.5 17223 1fjgP 88 4.13e+01 1emwA d.27.1.1 38444 1o7xD 377 4.18e+01 a.103.1.1 81174 1h0hA 977 4.22e+01 b.52.2.2,c.81.1.1 76435,76436 1jkvA 266 4.31e+01 a.25.1.3 71719 1o9iA 266 4.31e+01 a.25.1.3 92671 1pkn 530 4.32e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 2fp1A 166 4.36e+01 2f6lA 166 4.36e+01 2a3qA 170 4.44e+01 1fy7A 278 4.46e+01 1fy7A d.108.1.1 40817 1b7yA 350 4.51e+01 1pysA d.104.1.1 40776 1w7lA 422 4.60e+01 c.67.1.1 109226 1qtwA 285 4.60e+01 1qumA c.1.15.1 29392 1ytn 306 4.68e+01 1ytw c.45.1.2 32688 1lcjA 109 4.72e+01 1qadA d.93.1.1 40414 1eyvA 156 4.72e+01 1eyvA a.79.1.1 18446 1gu7A 364 4.83e+01 b.35.1.2,c.2.1.1 83321,83322 1z08A 170 4.84e+01 1vjeA 166 4.84e+01 d.185.1.2 100807 2gokA 429 4.98e+01 1ofdA 1520 5.01e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1ofgA 381 5.05e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1dk5A 322 5.06e+01 1dk5A a.65.1.1 18192 1yirA 408 5.08e+01 1gqeA 365 5.10e+01 e.38.1.1 70351 2gl5A 410 5.11e+01 1veaA 148 5.13e+01 d.275.1.1 108529 1innA 166 5.15e+01 1j98A d.185.1.2 62608 1ufoA 238 5.19e+01 c.69.1.27 99344 1jy2O 56 5.24e+01 h.1.8.1 67441 1jy3O 56 5.24e+01 h.1.8.1 67447 1q1vA 70 5.28e+01 a.159.4.1 104479 1kgnA 329 5.35e+01 a.25.1.2 68584 1a49A 530 5.36e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1ncx 162 5.36e+01 1ncx a.39.1.5 17222 1pmmA 466 5.41e+01 c.67.1.6 94901 1z6oA 212 5.42e+01 1h6dA 433 5.48e+01 c.2.1.3,d.81.1.5 65656,65657 1t3jA 96 5.51e+01 h.4.16.1 106356 1o04A 500 5.53e+01 c.82.1.1 86508 1ux8A 132 5.58e+01 1sfkA 76 5.59e+01 a.190.1.1 105488 1lckA 175 5.63e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1kq4A 232 5.65e+01 d.207.1.1 68791 1pzlA 237 5.75e+01 a.123.1.1 104393 1a93A 34 5.84e+01 1a93A h.1.3.1 45543 1ghhA 81 5.95e+01 1ghhA d.57.1.1 38940 1hynP 379 5.96e+01 1hynP d.112.1.2 61408 1zfpE 98 6.01e+01 1griA d.93.1.1 40465 1otkA 249 6.03e+01 a.25.1.2 93521 1sz2A 332 6.05e+01 1q18A 332 6.10e+01 c.55.1.7,c.55.1.7 104470,104471 1tgoA 773 6.18e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1f20A 435 6.24e+01 b.43.4.1,c.25.1.4 64932,64933 1onwA 390 6.26e+01 b.92.1.7,c.1.9.13 87172,87173 1jf4A 147 6.29e+01 a.1.1.2 71643 1gx5A 536 6.31e+01 e.8.1.4 70682 1a0nB 69 6.32e+01 1bbzA b.34.2.1 24469 1yg2A 179 6.35e+01 1jj2H 167 6.37e+01 1ffkF d.41.4.1 63093 1o5iA 249 6.37e+01 c.2.1.2 92499 1sjiA 350 6.44e+01 1hgeA 328 6.69e+01 1hgeA b.19.1.2 23816 1cuk 203 6.74e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1avsA 90 6.87e+01 1cll a.39.1.5 17226 1preB 470 6.88e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1gx3A 284 6.94e+01 d.3.1.5 70678 1xfxO 149 7.00e+01 2av5A 120 7.03e+01 1qhtA 775 7.03e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1gg3A 279 7.08e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1tzjA 338 7.09e+01 1lwjA 441 7.13e+01 b.71.1.1,c.1.8.1 74303,74304 1c2pA 576 7.16e+01 1quvA e.8.1.4 43117 1x1iA 752 7.18e+01 1wpiA 133 7.19e+01 1o26A 232 7.21e+01 d.207.1.1 86566 1pq4A 291 7.22e+01 c.92.2.2 94995 1gd2I 70 7.27e+01 1gd2I h.1.3.1 45532 1fvrA 327 7.29e+01 d.144.1.7 60047 1rqlA 267 7.32e+01 c.108.1.3 97750 1rgxA 114 7.33e+01 g.77.1.1 104932 1h2kA 349 7.38e+01 b.82.2.6 76572 2aotA 292 7.40e+01 1jj2L 194 7.42e+01 1ffkI d.12.1.2 63097 1zr6A 503 7.44e+01 1zymA 258 7.44e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1lm8V 160 7.45e+01 b.3.3.1 74035 1p27B 106 7.50e+01 d.58.7.1 93908 1j98A 157 7.52e+01 1j98A d.185.1.2 62755 1a2xA 159 7.54e+01 1ncx a.39.1.5 17251 1e7wA 291 7.54e+01 c.2.1.2 59373 1xi7A 61 7.65e+01 1a3yA 149 7.87e+01 1obpA b.60.1.1 27110 1keiA 316 7.91e+01 d.92.1.2 77349 1e5mA 416 7.95e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1nlwA 80 8.00e+01 a.38.1.1 80633 1b6cB 342 8.03e+01 1b6cB d.144.1.7 41673 1dzkA 157 8.14e+01 1obpA b.60.1.1 27096 1mioA 534 8.17e+01 1qguA c.92.2.3 35601 1z3iX 644 8.18e+01 1wguA 136 8.18e+01 1fezA 256 8.18e+01 1fezA c.108.1.3 43343 2cglA 489 8.24e+01 1ujwB 135 8.28e+01 h.4.9.1 99472 1k9dA 679 8.33e+01 c.1.8.10,d.92.2.2 77292,77293 1yua 122 8.38e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1tllA 688 8.38e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1ni5A 433 8.44e+01 c.26.2.5,d.229.1.1 80533,80534 3hmgA 328 8.46e+01 1hgeA b.19.1.2 23825 1qqcA 773 8.50e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1hz4A 373 8.57e+01 a.118.8.2 65960 1lre 81 8.63e+01 1lre a.13.1.1 16376 1nxcA 478 8.63e+01 a.102.2.1 92293 1td6A 306 8.69e+01 1gvmA 136 8.73e+01 b.109.1.1 70612 1vquA 374 8.78e+01 1nepA 130 8.81e+01 b.1.18.7 80440 1l9hA 349 8.86e+01 f.13.1.2 73720 2viuA 328 8.88e+01 1hgeA b.19.1.2 23797 2sttA 96 8.89e+01 1awcA a.4.5.21 16163 1v64A 108 8.93e+01 a.21.1.1 108392 1zuwA 272 8.94e+01 1py5A 326 8.96e+01 d.144.1.7 104389 2arpF 152 8.98e+01