# 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 2ap1A 327 3.19e-01 1xqaA 113 4.19e-01 1hfoA 113 8.09e-01 d.80.1.3 61006 1yrvA 169 1.06e+00 1f1sA 814 1.40e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 3proC 166 1.50e+00 3proC d.52.1.1,d.52.1.1 38812,38813 3proD 166 1.63e+00 3proC d.52.1.1,d.52.1.1 38814,38815 1wqgA 185 1.64e+00 1xawA 140 1.66e+00 1wzvA 155 1.78e+00 1ahr 146 2.11e+00 1cll a.39.1.5 17287 1hynP 379 3.57e+00 1hynP d.112.1.2 61408 1ufiA 64 3.76e+00 a.30.4.1 99336 2b20A 403 4.11e+00 1yirA 408 4.39e+00 1jy3O 56 4.42e+00 h.1.8.1 67447 1jy2O 56 4.62e+00 h.1.8.1 67441 1v0wA 506 4.92e+00 d.136.1.2,d.136.1.2 108220,108221 1k4nA 192 5.39e+00 d.32.1.5 72059 2ahqA 76 5.86e+00 1q2hA 69 5.97e+00 a.34.4.1 104498 1xttA 216 6.12e+00 1ggzA 148 6.31e+00 a.39.1.5 70176 2g0uA 92 6.31e+00 1s0yB 71 6.35e+00 d.80.1.1 98315 1sxjE 354 6.58e+00 a.80.1.1,c.37.1.20 106089,106090 1dd5A 185 6.84e+00 1dd5A d.67.3.1 39564 1zd9A 188 7.40e+00 1ww8A 439 7.74e+00 2fi9A 128 7.75e+00 1cll 148 7.92e+00 1cll a.39.1.5 17263 1y01A 102 8.68e+00 1z8uA 102 8.80e+00 3cln 148 8.88e+00 1cll a.39.1.5 17286 1wxcB 134 9.26e+00 1rp0A 284 9.31e+00 1yx1A 264 9.87e+00 1rypA 243 9.87e+00 1pmaA d.153.1.4 41932 1r85A 379 9.90e+00 c.1.8.3 104839 1dixA 208 9.92e+00 1bk7A d.124.1.1 41122 1f0iA 504 1.03e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1jkvA 266 1.06e+01 a.25.1.3 71719 1o9iA 266 1.08e+01 a.25.1.3 92671 1wgxA 73 1.09e+01 1fseA 74 1.22e+01 1fseA a.4.6.2 60000 1z08A 170 1.25e+01 1yh6A 179 1.26e+01 1mwwA 128 1.30e+01 d.80.1.4 91483 1p4kA 295 1.30e+01 d.153.1.5 87772 1ufoA 238 1.35e+01 c.69.1.27 99344 1tzpA 255 1.36e+01 d.65.1.3 107520 1g0uG 252 1.36e+01 d.153.1.4 41952 1tn4 159 1.40e+01 1ncx a.39.1.5 17248 1o7fA 469 1.44e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1osa 148 1.45e+01 1cll a.39.1.5 17300 1u9aA 160 1.47e+01 1u9aA d.20.1.1 38333 1wpaA 114 1.51e+01 1exrA 148 1.53e+01 1cll a.39.1.5 17299 1a8y 367 1.57e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1w9yA 319 1.59e+01 9gafA 295 1.60e+01 1apyA d.153.1.5 42008 2f6lA 166 1.61e+01 2fp1A 166 1.63e+01 1hizA 379 1.64e+01 c.1.8.3 65841 1k24A 253 1.66e+01 f.4.4.2 72002 1a93A 34 1.70e+01 1a93A h.1.3.1 45543 1twuA 139 1.77e+01 d.32.1.8 107413 1p4oA 322 1.84e+01 d.144.1.7 87775 2f3yA 148 1.88e+01 2db9A 149 1.89e+01 1gd8A 118 1.90e+01 d.188.1.1 60445 2occE 109 1.94e+01 2occE a.118.11.1 19224 1qltA 560 1.99e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1s1qA 145 2.02e+01 d.20.1.2 98351 1ni9A 338 2.06e+01 e.7.1.2 85739 2gqrA 237 2.07e+01 1w0bA 102 2.08e+01 a.7.11.1 108985 1t6cA 315 2.09e+01 c.55.1.8,c.55.1.8 106558,106559 1ov2A 99 2.10e+01 a.13.1.1 93580 1wsrA 375 2.12e+01 1nh2D 121 2.18e+01 a.32.1.1,b.56.1.1 91876,91877 1uzbA 516 2.19e+01 c.82.1.1 100220 1u0mA 382 2.23e+01 c.95.1.2,c.95.1.2 107557,107558 1ncx 162 2.25e+01 1ncx a.39.1.5 17222 1ni5A 433 2.25e+01 c.26.2.5,d.229.1.1 80533,80534 1tf1A 198 2.26e+01 d.110.2.2 106826 1v54E 109 2.28e+01 a.118.11.1 100326 2f5xA 312 2.30e+01 1u69A 163 2.33e+01 d.32.1.7 107699 2bjkA 516 2.35e+01 1keiA 316 2.39e+01 d.92.1.2 77349 1zoyC 140 2.43e+01 2c43A 323 2.50e+01 1nkpA 88 2.55e+01 a.38.1.1 80573 1u2eA 289 2.58e+01 1wp5A 323 2.59e+01 1ytfD 121 2.60e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1h16A 759 2.64e+01 c.7.1.1 76462 2cglA 489 2.67e+01 1h2kA 349 2.70e+01 b.82.2.6 76572 1x3lA 440 2.72e+01 1zb1A 392 2.75e+01 1hp0A 339 2.79e+01 c.70.1.1 65900 2b8iA 77 2.85e+01 1op1A 82 2.85e+01 a.13.1.1 93396 1eyvA 156 2.88e+01 1eyvA a.79.1.1 18446 1ek9A 428 2.91e+01 1ek9A f.5.1.1 43809 1preA 470 2.92e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1w1kA 560 2.93e+01 d.58.32.1,d.145.1.1 109059,109060 1q5yA 85 2.94e+01 d.58.18.4 95950 1top 162 2.94e+01 1ncx a.39.1.5 17223 2fjlA 150 3.03e+01 2cohA 202 3.04e+01 1fzqA 181 3.06e+01 1hurA c.37.1.8 32060 1cm5A 759 3.08e+01 1cm5A c.7.1.1 30671 1k1fA 72 3.09e+01 a.147.1.1 68007 6tmnE 316 3.11e+01 1hyt d.92.1.2 59071 1q1lA 401 3.17e+01 d.258.1.1 95591 1kq4A 232 3.18e+01 d.207.1.1 68791 1z52A 470 3.21e+01 2pflA 759 3.25e+01 1cm5A c.7.1.1 30675 3pflA 759 3.26e+01 1cm5A c.7.1.1 30673 1rqlA 267 3.30e+01 c.108.1.3 97750 1o97C 264 3.32e+01 c.26.2.3 81232 1zymA 258 3.34e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1w3fA 315 3.35e+01 1t3jA 96 3.38e+01 h.4.16.1 106356 1rgxA 114 3.45e+01 g.77.1.1 104932 1jf4A 147 3.50e+01 a.1.1.2 71643 1u5uA 374 3.50e+01 1vh4A 435 3.56e+01 b.80.6.1 100640 1aurA 218 3.61e+01 1auoA c.69.1.14 34718 1mzeA 351 3.66e+01 b.82.2.6 79694 1nxcA 478 3.68e+01 a.102.2.1 92293 1gm7B 557 3.70e+01 2a3qA 170 3.76e+01 1xn9A 101 3.78e+01 1veaA 148 3.83e+01 d.275.1.1 108529 2grrA 161 3.86e+01 1lre 81 3.91e+01 1lre a.13.1.1 16376 1u08A 386 3.91e+01 c.67.1.1 107543 1lrzA 426 3.94e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1jqeA 292 3.95e+01 c.66.1.19 71789 1ois 223 3.96e+01 1a36A e.15.1.1 43267 1tzbA 302 4.02e+01 c.80.1.1 107470 1x9iA 302 4.02e+01 1ni4B 341 4.13e+01 c.36.1.7,c.48.1.2 85729,85730 1eqfA 280 4.14e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1k8rB 110 4.15e+01 d.15.1.5 72180 1g4yR 148 4.35e+01 1cll a.39.1.5 60252 1otjA 283 4.37e+01 b.82.2.5 93517 1vkuA 100 4.39e+01 a.28.1.1 108690 1a87 321 4.42e+01 1a87 f.1.1.1 43380 1otsA 465 4.50e+01 f.20.1.1 87415 1swvA 267 4.50e+01 2tmnE 316 4.54e+01 1hyt d.92.1.2 59055 1h0hA 977 4.57e+01 b.52.2.2,c.81.1.1 76435,76436 2abwA 227 4.58e+01 2ah6A 208 4.60e+01 2bydA 323 4.68e+01 1hozA 339 4.68e+01 c.70.1.1 65898 1e8gA 560 4.71e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 2afwA 329 4.73e+01 1c25 161 4.75e+01 1c25 c.46.1.1 32698 1eza 259 4.75e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1gm9B 557 4.75e+01 1a3s 160 4.75e+01 1u9aA d.20.1.1 38335 1hyt 316 4.75e+01 1hyt d.92.1.2 59005 1pq4A 291 4.81e+01 c.92.2.2 94995 2gm3A 175 4.83e+01 1pysA 350 4.83e+01 1pysA d.104.1.1 40775 1ynmA 247 4.91e+01 1mzjA 339 4.95e+01 c.95.1.2,c.95.1.2 79700,79701 2aegA 268 4.96e+01 1vaoA 560 5.04e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1iz0A 302 5.10e+01 b.35.1.2,c.2.1.1 83821,83822 1zbtA 371 5.12e+01 1xzzA 246 5.12e+01 1ux8A 132 5.14e+01 1auoA 218 5.19e+01 1auoA c.69.1.14 34716 1i2oA 316 5.22e+01 1onrA c.1.10.1 61574 1uq5A 263 5.23e+01 d.165.1.1 99778 1rpmA 278 5.31e+01 2shpA c.45.1.2 32679 1avsA 90 5.31e+01 1cll a.39.1.5 17226 1onrA 316 5.35e+01 1onrA c.1.10.1 29169 1eg2A 319 5.37e+01 1eg2A c.66.1.11 34249 1llmC 88 5.37e+01 g.37.1.1,g.37.1.1 91059,91060 1ajqB 557 5.39e+01 1ajqB 1xsjA 778 5.41e+01 2fhfA 1083 5.42e+01 1ift 263 5.49e+01 1mrj d.165.1.1 42211 2aotA 292 5.54e+01 1a92A 50 5.56e+01 1a92A h.4.6.1 45791 1gkfB 557 5.66e+01 1pnkB 557 5.67e+01 1ajqB 1t0aA 159 5.70e+01 1o8vA 134 5.74e+01 b.60.1.2 86680 1otfA 62 5.74e+01 1otfA d.80.1.1 39820 1tjlA 151 5.75e+01 a.2.14.1,g.39.1.13 107027,107028 1c9bB 180 5.75e+01 1ytbA d.129.1.1,d.129.1.1 41216,41217 1jf3A 147 5.78e+01 a.1.1.2 71642 2f2hA 773 5.81e+01 1qe5A 266 5.84e+01 1b8oA c.56.2.1 33784 8tlnE 316 5.85e+01 1hyt d.92.1.2 59075 1gqwA 283 5.99e+01 b.82.2.5 70377 1ak8 76 5.99e+01 1cll a.39.1.5 17281 1szoA 257 6.02e+01 c.14.1.3 106164 1gy9A 283 6.03e+01 b.82.2.5 70742 1zvkA 358 6.13e+01 2ga1A 106 6.21e+01 1d2vC 466 6.22e+01 1mhlC 1gk9B 557 6.22e+01 2h88C 140 6.22e+01 1obs 267 6.24e+01 1mrj d.165.1.1 42213 1cxpC 466 6.25e+01 1mhlC 1sazA 381 6.29e+01 1fxtA 149 6.36e+01 d.20.1.1 65055 1oxwA 373 6.44e+01 c.19.1.3 87539 1uqrA 154 6.44e+01 c.23.13.1 99779 1nw8A 319 6.45e+01 c.66.1.11 86292 1kllA 130 6.46e+01 d.32.1.2 72720 1tueA 212 6.53e+01 c.37.1.20 107323 1e3aB 560 6.54e+01 1ajqB 1np7A 489 6.55e+01 a.99.1.1,c.28.1.1 80677,80678 1jroB 777 6.56e+01 d.41.1.1,d.133.1.1 67141,67142 1z6uA 150 6.58e+01 1yf9A 171 6.59e+01 1pl5A 142 6.60e+01 h.1.23.1 104186 1fw9A 164 6.62e+01 1fw9A d.190.1.1 60059 1kpkA 473 6.64e+01 f.20.1.1 68776 4bcl 366 6.65e+01 4bcl b.75.1.1 27968 1gyxA 76 6.65e+01 d.80.1.1 76387 2fbwC 141 6.69e+01 1gehA 444 6.75e+01 c.1.14.1,d.58.9.1 65181,65182 1h4wA 224 6.83e+01 b.47.1.2 65622 1m7yA 435 6.90e+01 c.67.1.4 78761 1kshA 186 6.96e+01 c.37.1.8 72914 2g5cA 281 6.98e+01 2gokA 429 7.07e+01 1ezwA 349 7.10e+01 1ezwA c.1.16.3 29558 1mhlC 466 7.14e+01 1mhlC 1qmuA 380 7.15e+01 1qmuA b.3.2.1,c.56.5.1 22534,33827 1w6sB 74 7.19e+01 1h8lA 380 7.19e+01 b.3.2.1,c.56.5.1 65737,65738 2ftuA 118 7.27e+01 1lmeA 176 7.34e+01 d.167.1.1 84629 1dj7A 117 7.35e+01 1dj7A g.36.1.1 44997 1ofgA 381 7.35e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1gt91 357 7.38e+01 1f7tA 122 7.39e+01 1f7lA d.150.1.2 59667 1t6sA 162 7.42e+01 1l9mA 692 7.47e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1tu3F 79 7.49e+01 1p4dA 330 7.49e+01 d.89.1.5 94101 1mnmC 87 7.52e+01 1akhB a.4.1.1 15983 2carA 196 7.61e+01 1ursA 402 7.65e+01 c.94.1.1 99833 1fzyA 149 7.66e+01 d.20.1.1 65072 1o26A 232 7.75e+01 d.207.1.1 86566 1i3uA 127 7.82e+01 1gc1H b.1.1.1 61636 1fezA 256 7.84e+01 1fezA c.108.1.3 43343 1gttA 429 7.92e+01 d.177.1.1,d.177.1.1 70529,70530 1rxdA 159 7.92e+01 1b8gA 429 8.05e+01 1b8gA c.67.1.4 34499 1apf 49 8.10e+01 1ahl g.9.1.1 44602 1emwA 88 8.11e+01 1emwA d.27.1.1 38448 1akr 147 8.11e+01 1rcf c.23.5.1 31152 1dzkA 157 8.18e+01 1obpA b.60.1.1 27096 1hylA 230 8.19e+01 5ptp b.47.1.2 26076 1oqcA 125 8.28e+01 a.24.15.1 87264 1jsdA 319 8.28e+01 b.19.1.2 63258 1gd2I 70 8.37e+01 1gd2I h.1.3.1 45532 1tib 269 8.39e+01 3tgl c.69.1.17 34738 1f7lA 121 8.42e+01 1f7lA d.150.1.2 59666 2fcwA 109 8.42e+01 1wusA 180 8.46e+01 1gp4A 356 8.48e+01 b.82.2.1 65439 1nrjA 158 8.51e+01 d.110.4.4 86124 1akt 147 8.57e+01 5nul c.23.5.1 31157 1vhnA 318 8.64e+01 c.1.4.1 100693 1s2xA 206 8.69e+01 a.47.3.1 105229 1c4zD 154 8.70e+01 1u9aA d.20.1.1 38331 1gp6A 356 8.76e+01 b.82.2.1 65441 1o20A 427 8.79e+01 c.82.1.1 86556 1wozA 177 8.79e+01 1l5jA 865 8.80e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1z0wA 207 8.82e+01 1yts 278 8.82e+01 1ytw c.45.1.2 32690 1jihA 531 8.83e+01 d.240.1.1,e.8.1.7 90374,90375 1i7oA 429 8.94e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1zckA 154 8.96e+01 1s4kA 120 8.96e+01 a.35.1.6 105254 1zac 90 8.98e+01 1ncx a.39.1.5 17236