# 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.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 2.71e-03 1rypA 243 3.52e-02 1pmaA d.153.1.4 41932 1g0uG 252 4.27e-02 d.153.1.4 41952 1xqaA 113 1.29e-01 1yrvA 169 4.22e-01 1hfoA 113 6.38e-01 d.80.1.3 61006 1gd8A 118 6.56e-01 d.188.1.1 60445 1ahr 146 9.20e-01 1cll a.39.1.5 17287 1wzvA 155 9.46e-01 1qhbA 596 1.21e+00 1qhbA a.111.1.2 19055 1jl5A 454 1.40e+00 c.10.2.6 66830 1o7fA 469 1.44e+00 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1g9uA 454 1.49e+00 c.10.2.6 65172 1u08A 386 1.52e+00 c.67.1.1 107543 2b20A 403 1.57e+00 1pwxA 254 1.98e+00 c.2.1.2 95262 2g0uA 92 1.98e+00 1yx1A 264 2.07e+00 1cll 148 2.08e+00 1cll a.39.1.5 17263 1ggzA 148 2.10e+00 a.39.1.5 70176 1wxcB 134 2.17e+00 2fi9A 128 2.43e+00 1zmtA 254 2.52e+00 1xttA 216 2.64e+00 1eqfA 280 2.69e+00 1eqfA a.29.2.1,a.29.2.1 16972,16973 3cln 148 2.84e+00 1cll a.39.1.5 17286 1fseA 74 2.84e+00 1fseA a.4.6.2 60000 1ytfD 121 2.92e+00 1ytfD a.32.1.1,b.56.1.1 16998,27011 2gqrA 237 3.09e+00 1ufiA 64 3.11e+00 a.30.4.1 99336 1k4nA 192 3.20e+00 d.32.1.5 72059 1wp5A 323 3.22e+00 1xawA 140 3.36e+00 2ahqA 76 3.37e+00 1jy3O 56 3.42e+00 h.1.8.1 67447 1exrA 148 3.49e+00 1cll a.39.1.5 17299 2gokA 429 3.55e+00 1top 162 3.58e+00 1ncx a.39.1.5 17223 1jy2O 56 3.62e+00 h.1.8.1 67441 1osa 148 3.86e+00 1cll a.39.1.5 17300 1nh2D 121 3.92e+00 a.32.1.1,b.56.1.1 91876,91877 1q2hA 69 3.97e+00 a.34.4.1 104498 1e5mA 416 4.40e+00 1dd8A c.95.1.1,c.95.1.1 58973,58974 1ncx 162 4.69e+00 1ncx a.39.1.5 17222 1s0yB 71 4.69e+00 d.80.1.1 98315 3proC 166 4.86e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1y01A 102 4.91e+00 1zd9A 188 4.96e+00 1hynP 379 5.17e+00 1hynP d.112.1.2 61408 2bydA 323 5.23e+00 2db9A 149 5.28e+00 1xkpA 246 5.33e+00 1w0bA 102 5.50e+00 a.7.11.1 108985 1fzqA 181 5.72e+00 1hurA c.37.1.8 32060 3proD 166 6.19e+00 3proC d.52.1.1,d.52.1.1 38814,38815 2bjkA 516 6.32e+00 2c43A 323 6.61e+00 1z8uA 102 6.65e+00 1r85A 379 7.46e+00 c.1.8.3 104839 2f6lA 166 7.49e+00 2cglA 489 7.54e+00 1ytw 306 7.66e+00 1ytw c.45.1.2 32689 1v0wA 506 7.83e+00 d.136.1.2,d.136.1.2 108220,108221 1lcjA 109 7.92e+00 1qadA d.93.1.1 40414 1uzbA 516 7.92e+00 c.82.1.1 100220 1f1sA 814 8.21e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 2aegA 268 8.29e+00 1gx1A 160 8.46e+00 d.79.5.1 70675 1nxcA 478 8.83e+00 a.102.2.1 92293 1fzyA 149 9.11e+00 d.20.1.1 65072 1up8A 598 9.19e+00 a.111.1.2 99710 2fp1A 166 9.33e+00 1qgtA 149 9.71e+00 1qgtA a.62.1.1 18135 1eyvA 156 9.75e+00 1eyvA a.79.1.1 18446 1xzzA 246 9.88e+00 1fgyA 127 9.94e+00 1faoA b.55.1.1 26976 1tf1A 198 1.01e+01 d.110.2.2 106826 1z52A 470 1.02e+01 1ux8A 132 1.04e+01 1u9aA 160 1.04e+01 1u9aA d.20.1.1 38333 1pq4A 291 1.06e+01 c.92.2.2 94995 2fjlA 150 1.07e+01 1c9bB 180 1.09e+01 1ytbA d.129.1.1,d.129.1.1 41216,41217 2ajrA 331 1.11e+01 1v54E 109 1.13e+01 a.118.11.1 100326 1preA 470 1.14e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1f0iA 504 1.18e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1hizA 379 1.20e+01 c.1.8.3 65841 2d1yA 256 1.26e+01 1a3s 160 1.26e+01 1u9aA d.20.1.1 38335 2f3yA 148 1.27e+01 1lkkA 105 1.27e+01 1lckA d.93.1.1 40412 2occE 109 1.29e+01 2occE a.118.11.1 19224 1tn4 159 1.29e+01 1ncx a.39.1.5 17248 1rp0A 284 1.32e+01 1zb1A 392 1.33e+01 1ww8A 439 1.35e+01 1c4zD 154 1.38e+01 1u9aA d.20.1.1 38331 1veaA 148 1.39e+01 d.275.1.1 108529 1qk3A 233 1.40e+01 1qk3A c.61.1.1 34031 1preB 470 1.40e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1q1lA 401 1.44e+01 d.258.1.1 95591 1ek9A 428 1.44e+01 1ek9A f.5.1.1 43809 1fxtA 149 1.47e+01 d.20.1.1 65055 1dbrA 231 1.49e+01 1qk3A c.61.1.1 34041 1sxjE 354 1.54e+01 a.80.1.1,c.37.1.20 106089,106090 1up6A 416 1.54e+01 c.2.1.5,d.162.1.2 107976,107977 1yirA 408 1.55e+01 1yts 278 1.56e+01 1ytw c.45.1.2 32690 1wqgA 185 1.58e+01 1pkn 530 1.62e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1zac 90 1.71e+01 1ncx a.39.1.5 17236 1jy8A 159 1.73e+01 d.79.5.1 67452 2gupA 292 1.75e+01 1jkvA 266 1.80e+01 a.25.1.3 71719 1ni9A 338 1.82e+01 e.7.1.2 85739 1i2oA 316 1.82e+01 1onrA c.1.10.1 61574 2fa8A 105 1.82e+01 1rqlA 267 1.83e+01 c.108.1.3 97750 1mwwA 128 1.87e+01 d.80.1.4 91483 2grrA 161 1.87e+01 1kllA 130 1.90e+01 d.32.1.2 72720 1lyvA 306 1.92e+01 c.45.1.2 74348 1u7kA 131 1.93e+01 1g4yR 148 1.97e+01 1cll a.39.1.5 60252 1obs 267 2.05e+01 1mrj d.165.1.1 42213 1a93A 34 2.06e+01 1a93A h.1.3.1 45543 1o9iA 266 2.08e+01 a.25.1.3 92671 1wgxA 73 2.09e+01 1dk5A 322 2.09e+01 1dk5A a.65.1.1 18192 5rubA 490 2.10e+01 1burA c.1.14.1,d.58.9.1 29382,39288 1irxA 523 2.12e+01 a.97.1.2,c.26.1.1 71378,71379 1sspE 223 2.13e+01 3eugA c.18.1.1 31009 2fulA 178 2.13e+01 1efuB 282 2.13e+01 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 1p4kA 295 2.14e+01 d.153.1.5 87772 1t7lA 766 2.15e+01 1szoA 257 2.15e+01 c.14.1.3 106164 1ufoA 238 2.19e+01 c.69.1.27 99344 1a8y 367 2.21e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1v2dA 381 2.24e+01 c.67.1.1 108281 1onrA 316 2.24e+01 1onrA c.1.10.1 29169 1ift 263 2.25e+01 1mrj d.165.1.1 42211 1nrkA 328 2.25e+01 b.44.2.1,d.250.1.1 92089,92090 1jqeA 292 2.28e+01 c.66.1.19 71789 1nkpA 88 2.29e+01 a.38.1.1 80573 1cdwA 179 2.34e+01 1ytbA d.129.1.1,d.129.1.1 41212,41213 1hmpA 217 2.35e+01 1qk3A c.61.1.1 34075 1q1vA 70 2.37e+01 a.159.4.1 104479 1yptA 305 2.38e+01 1ytw c.45.1.2 32686 1jf4A 147 2.51e+01 a.1.1.2 71643 1nnwA 252 2.56e+01 d.159.1.5 80674 1wpaA 114 2.60e+01 1p5zB 263 2.61e+01 c.37.1.1 87815 1k24A 253 2.62e+01 f.4.4.2 72002 1gx3A 284 2.62e+01 d.3.1.5 70678 1uq5A 263 2.65e+01 d.165.1.1 99778 1j5sA 463 2.65e+01 c.1.9.8 71580 2b8iA 77 2.69e+01 2g50A 530 2.69e+01 1ytn 306 2.76e+01 1ytw c.45.1.2 32688 1a2xA 159 2.78e+01 1ncx a.39.1.5 17251 1u2eA 289 2.79e+01 1azgB 67 2.84e+01 1bbzA b.34.2.1 24471 1t6sA 162 2.86e+01 1wpuA 147 2.97e+01 1fsgA 233 2.98e+01 1qk3A c.61.1.1 34029 1lre 81 3.00e+01 1lre a.13.1.1 16376 9gafA 295 3.02e+01 1apyA d.153.1.5 42008 1otfA 62 3.08e+01 1otfA d.80.1.1 39820 1ov2A 99 3.08e+01 a.13.1.1 93580 1op1A 82 3.10e+01 a.13.1.1 93396 1efnA 59 3.11e+01 1bbzA b.34.2.1 24465 2rusB 490 3.11e+01 1burA c.1.14.1,d.58.9.1 29385,39291 1z7gA 217 3.12e+01 1avzC 57 3.16e+01 1bbzA b.34.2.1 24467 1o97C 264 3.21e+01 c.26.2.3 81232 1cqkA 101 3.28e+01 1cqkA b.1.1.2 21547 1vlyA 338 3.28e+01 b.44.2.1,d.250.1.1 108871,108872 1rusA 490 3.29e+01 1burA c.1.14.1,d.58.9.1 29388,39294 1pytA 94 3.33e+01 1pytA d.58.3.1 39064 1xi7A 61 3.37e+01 1c25 161 3.39e+01 1c25 c.46.1.1 32698 1euvB 86 3.39e+01 1a5r d.15.1.1 37598 1wsrA 375 3.40e+01 1yh6A 179 3.41e+01 1a0nB 69 3.45e+01 1bbzA b.34.2.1 24469 1w23A 360 3.45e+01 1o26A 232 3.45e+01 d.207.1.1 86566 1yh2A 175 3.48e+01 1zclA 180 3.49e+01 1qk4A 233 3.52e+01 1qk3A c.61.1.1 34037 1zuwA 272 3.54e+01 1ak8 76 3.57e+01 1cll a.39.1.5 17281 1kr4A 125 3.59e+01 d.58.5.2 72889 1x1iA 752 3.62e+01 1larA 575 3.63e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1ezwA 349 3.68e+01 1ezwA c.1.16.3 29558 1oxwA 373 3.75e+01 c.19.1.3 87539 1dd5A 185 3.77e+01 1dd5A d.67.3.1 39564 1ytbA 180 3.80e+01 1ytbA d.129.1.1,d.129.1.1 41276,41277 1fezA 256 3.81e+01 1fezA c.108.1.3 43343 1lckA 175 3.83e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1ni5A 433 3.85e+01 c.26.2.5,d.229.1.1 80533,80534 1vkuA 100 3.85e+01 a.28.1.1 108690 1k1fA 72 3.86e+01 a.147.1.1 68007 2aotA 292 3.90e+01 1guzA 310 3.90e+01 c.2.1.5,d.162.1.1 65586,65587 1swvA 267 3.91e+01 1s4kA 120 3.92e+01 a.35.1.6 105254 1o7xC 377 3.94e+01 a.103.1.1 81173 1ajqB 557 3.97e+01 1ajqB 4bcl 366 3.98e+01 4bcl b.75.1.1 27968 1o8uA 257 3.99e+01 c.14.1.3 81194 1urrA 102 4.01e+01 d.58.10.1 107998 1stzA 338 4.04e+01 a.4.5.51,d.110.2.3 106009,106010 1a87 321 4.04e+01 1a87 f.1.1.1 43380 1ta0A 197 4.08e+01 c.108.1.16 106729 1shfA 59 4.10e+01 1bbzA b.34.2.1 24462 1z90A 469 4.12e+01 2afwA 329 4.13e+01 1d2vC 466 4.17e+01 1mhlC 1rpmA 278 4.18e+01 2shpA c.45.1.2 32679 2h88C 140 4.18e+01 2f4mA 295 4.19e+01 2pflA 759 4.20e+01 1cm5A c.7.1.1 30675 1ej8A 140 4.20e+01 1qupA b.1.8.1 22300 1yfoA 302 4.22e+01 2shpA c.45.1.2 32681 1kq4A 232 4.22e+01 d.207.1.1 68791 1b7yA 350 4.22e+01 1pysA d.104.1.1 40776 3pflA 759 4.31e+01 1cm5A c.7.1.1 30673 1wmqA 147 4.33e+01 1u5uA 374 4.34e+01 1gm9B 557 4.36e+01 2f5xA 312 4.38e+01 1fvrA 327 4.47e+01 d.144.1.7 60047 1t3jA 96 4.48e+01 h.4.16.1 106356 1yua 122 4.48e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1uddA 226 4.53e+01 a.132.1.3 107776 1lm8B 118 4.54e+01 d.15.1.1 74033 1qydA 313 4.60e+01 c.2.1.2 96583 1akz 223 4.63e+01 3eugA c.18.1.1 31007 1gkfB 557 4.64e+01 1o7xB 377 4.67e+01 a.103.1.1 81172 1jf3A 147 4.68e+01 a.1.1.2 71642 1r62A 160 4.70e+01 d.122.1.3 104816 1vcvA 226 4.76e+01 1v5sA 126 4.83e+01 d.129.6.1 108384 2ftuA 118 4.84e+01 1wzoA 246 4.84e+01 1dusA 194 4.85e+01 1dusA c.66.1.4 34182 1diwA 441 4.85e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1h16A 759 4.86e+01 c.7.1.1 76462 1j0mA 752 4.87e+01 a.102.3.2,b.24.1.1,b.30.5.2 83910,83911,83912 1ki1B 352 4.88e+01 a.87.1.1,b.55.1.1 72497,72498 1u69A 163 4.88e+01 d.32.1.7 107699 1egr 85 4.89e+01 1kte c.47.1.1 32765 1div 149 4.93e+01 1div d.99.1.1,d.100.1.1 40692,40693 1iu9A 111 4.93e+01 c.78.2.1 90694 1zbtA 371 4.96e+01 1cm5A 759 4.97e+01 1cm5A c.7.1.1 30671 1rdfA 267 5.01e+01 c.108.1.3 104884 1gk9B 557 5.15e+01 1zx2A 147 5.15e+01 1gm7B 557 5.20e+01 1ndbA 596 5.22e+01 c.43.1.3,c.43.1.3 80411,80412 1a49A 530 5.22e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1x24A 180 5.24e+01 1eluB 390 5.25e+01 1elqA c.67.1.3 34435 1a8d 452 5.26e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1lmeA 176 5.27e+01 d.167.1.1 84629 1mut 129 5.29e+01 1tum d.113.1.1 40921 1s3sG 127 5.33e+01 d.15.1.2 98457 1gyxA 76 5.41e+01 d.80.1.1 76387 2a0iA 330 5.49e+01 1z08A 170 5.58e+01 1kxoA 184 5.59e+01 b.60.1.1 84475 1q5yA 85 5.60e+01 d.58.18.4 95950 2pvaA 345 5.61e+01 3pvaA d.153.1.3 41850 1d0hA 469 5.65e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1o5iA 249 5.67e+01 c.2.1.2 92499 1dlyA 164 5.71e+01 1dlyA a.1.1.1 14983 1p4dA 330 5.72e+01 d.89.1.5 94101 1xesA 413 5.74e+01 1kshA 186 5.76e+01 c.37.1.8 72914 1hb6A 86 5.76e+01 a.11.1.1 70959 1w9yA 319 5.76e+01 2fcwA 109 5.90e+01 1z6gA 218 5.91e+01 1d8hA 311 5.94e+01 1d8iA d.63.1.1 39544 2gmyA 153 5.95e+01 1fa0B 537 5.95e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1pnkB 557 6.01e+01 1ajqB 1k9dA 679 6.04e+01 c.1.8.10,d.92.2.2 77292,77293 1e6yA 569 6.07e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1mejA 223 6.08e+01 c.65.1.1 79029 3pvaA 335 6.10e+01 3pvaA d.153.1.3 41854 1r59O 505 6.11e+01 1e7wA 291 6.17e+01 c.2.1.2 59373 1cxpC 466 6.19e+01 1mhlC 2g8lA 299 6.19e+01 1jsdA 319 6.21e+01 b.19.1.2 63258 1ybxA 143 6.23e+01 1yu3A 381 6.27e+01 2ga1A 106 6.27e+01 1mhlC 466 6.28e+01 1mhlC 1vcbA 118 6.42e+01 1vcbA d.15.1.1 37603 1d8iA 311 6.44e+01 1d8iA d.63.1.1 39541 1ytbB 180 6.46e+01 1ytbA d.129.1.1,d.129.1.1 41278,41279 1w7lA 422 6.47e+01 c.67.1.1 109226 1tzbA 302 6.47e+01 c.80.1.1 107470 1yu4A 381 6.48e+01 1elqA 390 6.52e+01 1elqA c.67.1.3 34436 1z5yE 149 6.55e+01 1x9iA 302 6.62e+01 1otkA 249 6.62e+01 a.25.1.2 93521 1nlwA 80 6.64e+01 a.38.1.1 80633 1ynmA 247 6.66e+01 1zymA 258 6.73e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 2fbwC 141 6.78e+01 1utyA 187 6.78e+01 b.147.1.1 108036 1z3iX 644 6.78e+01 1f7tA 122 6.83e+01 1f7lA d.150.1.2 59667 2gasA 307 6.84e+01 1yu0A 381 6.86e+01 1rxdA 159 6.87e+01 1dj7A 117 6.90e+01 1dj7A g.36.1.1 44997 1t00A 112 6.95e+01 1qipA 183 7.02e+01 1qipA d.32.1.1 38470 1zvkA 358 7.08e+01 1aoiC 116 7.09e+01 1aoiC a.22.1.1 16440 1ywnA 316 7.11e+01 1xn9A 101 7.11e+01 1zckA 154 7.11e+01 2fnjB 118 7.13e+01 1e3aB 560 7.14e+01 1ajqB 1yu2A 381 7.17e+01 1avsA 90 7.19e+01 1cll a.39.1.5 17226 1qhhA 167 7.21e+01 1pjr c.37.1.19 32393 2eifA 136 7.22e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2a3qA 170 7.22e+01 1ak2 233 7.29e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1cb1 78 7.31e+01 4icb a.39.1.1 17156 1meoA 209 7.31e+01 c.65.1.1 79035 1w6sB 74 7.31e+01 1qe5A 266 7.32e+01 1b8oA c.56.2.1 33784 1q3iA 214 7.34e+01 d.220.1.1 104524 1uxtA 501 7.43e+01 c.82.1.1 108125 1up7A 417 7.50e+01 1kppA 145 7.51e+01 d.20.1.2 72846 1q7hA 153 7.52e+01 b.122.1.1,d.17.6.2 96042,96043 1nvvS 481 7.57e+01 a.117.1.1 86279 1ul7A 102 7.59e+01 d.129.6.1 99540 1as8A 343 7.61e+01 1nif b.6.1.3,b.6.1.3 23074,23075 2f9zC 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