# List of top-scoring protein chains for t04-100-30-str2-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 1jpaA 312 8.45e-66 d.144.1.7 67011 1opjA 293 7.51e-64 d.144.1.7 87230 1ir3A 306 4.82e-63 1fmk d.144.1.7 41702 1p4oA 322 2.79e-62 d.144.1.7 87775 1t46A 313 1.27e-60 d.144.1.7 106397 1fgkA 310 3.18e-60 1fgkA d.144.1.7 41693 1qpcA 279 3.29e-60 1fgkA d.144.1.7 41685 1r0pA 312 4.15e-58 d.144.1.7 96734 1mp8A 281 1.40e-57 d.144.1.7 91384 1fvrA 327 2.12e-57 d.144.1.7 60047 1u59A 287 1.11e-56 d.144.1.7 107681 1u46A 291 2.69e-56 d.144.1.7 107656 1ywnA 316 6.91e-56 1xbbA 291 7.14e-56 2b7aA 293 1.19e-53 2evaA 307 5.76e-44 1mq4A 272 8.15e-36 d.144.1.7 91391 2f57A 317 3.97e-35 1yhvA 297 5.86e-35 1f3mC 297 3.51e-34 1hcl d.144.1.7 41677 1xjdA 345 1.09e-33 1t4hA 290 3.23e-33 d.144.1.7 106420 2c30A 321 4.49e-33 2bfxA 284 1.16e-32 1ia8A 289 2.16e-31 1ia8A d.144.1.7 62112 1o6lA 337 2.25e-31 d.144.1.7 81092 1xh9A 350 3.54e-31 2bdwA 362 1.08e-30 1gz8A 299 1.11e-30 d.144.1.7 83405 1hcl 298 2.12e-30 1hcl d.144.1.7 41593 1h1wA 289 2.69e-30 d.144.1.7 83460 1uu3A 310 3.04e-30 d.144.1.7 99999 1apmE 350 3.17e-30 1cdkA d.144.1.7 41628 1py5A 326 3.23e-30 d.144.1.7 104389 1vjyA 303 4.07e-30 d.144.1.7 108633 2a19B 284 4.73e-30 1rdqE 350 4.89e-30 d.144.1.7 97314 1s9jA 341 5.34e-30 1o6yA 299 5.76e-30 d.144.1.7 81106 1jksA 294 1.93e-29 d.144.1.7 71710 2eueA 279 2.31e-29 2bvaA 292 3.24e-29 1zrzA 364 4.11e-29 1zy4A 303 4.12e-29 1blxA 326 4.52e-29 1hcl d.144.1.7 41596 1phk 298 3.53e-28 1cdkA d.144.1.7 41635 1vzoA 355 4.82e-28 d.144.1.7 108971 3erk 364 1.59e-27 1hcl d.144.1.7 41654 1tvoA 368 1.66e-27 1p4fA 293 2.83e-27 d.144.1.7 104063 1omwA 689 1.08e-26 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1pmnA 364 1.74e-26 d.144.1.7 94907 2b9hA 353 2.30e-26 1pme 380 4.95e-26 1hcl d.144.1.7 41653 1wbsA 360 1.15e-25 1x8bA 289 1.49e-25 2ac5A 316 1.52e-25 1zzlA 351 1.96e-25 1tkiA 321 2.29e-25 1tkiA d.144.1.7 41638 1xwsA 313 2.52e-25 1r3cA 366 2.77e-25 d.144.1.7 96906 2bikB 313 5.11e-25 1zz2A 360 5.38e-25 1ywrA 360 1.79e-24 2gfsA 372 4.85e-24 2ac3A 316 5.73e-24 1j1bA 420 1.88e-22 d.144.1.7 90758 1ymiA 334 2.70e-22 1z57A 339 1.68e-21 1ckiA 317 5.06e-21 1csn d.144.1.7 41660 2eu9A 355 1.73e-20 1om1A 332 6.22e-20 d.144.1.7 93347 1m2rA 327 1.00e-19 d.144.1.7 84760 1csn 298 2.84e-18 1csn d.144.1.7 41664 1howA 373 3.86e-18 1hcl d.144.1.7 41679 1q8yA 373 9.22e-18 d.144.1.7 96234 1wbpA 397 7.68e-17 1zarA 282 3.80e-06 1tqmA 282 4.36e-06 a.4.5.56,d.144.1.9 107236,107237 1vgjA 184 1.25e-02 1je0A 236 2.40e-02 c.56.2.1 66581 1vdxA 184 3.44e-02 1jysA 242 6.40e-02 c.56.2.1 77216 1z5oA 242 1.64e-01 1ako 268 1.91e-01 1ako d.151.1.1 41779 1nd4A 264 2.31e-01 d.144.1.6 91815 1z5nA 242 2.72e-01 1a68 95 3.70e-01 1t1dA d.42.1.2 38639 1q52A 314 4.27e-01 c.14.1.3 95846 1dsxA 87 5.07e-01 1t1dA d.42.1.2 38644 1t1dA 100 5.53e-01 1t1dA d.42.1.2 38637 1odkA 235 6.78e-01 c.56.2.1 86863 1lyvA 306 8.42e-01 c.45.1.2 74348 1i9zA 347 8.69e-01 1i9yA d.151.1.2 62102 1ytw 306 9.56e-01 1ytw c.45.1.2 32689 1xe0A 114 9.98e-01 1jl2A 156 1.12e+00 c.55.3.1 66822 1quqA 129 1.20e+00 1quqA b.40.4.3 25303 1rybA 212 1.29e+00 c.56.3.1 98098 2ajrA 331 1.33e+00 1ecpA 238 1.55e+00 1ecpA c.56.2.1 33775 1bsg 266 1.86e+00 1btl e.3.1.1 42729 1zthA 258 1.92e+00 1ogaD 215 1.93e+00 b.1.1.1,b.1.1.2 86990,86991 1widA 130 1.96e+00 1ermA 263 2.06e+00 1btl e.3.1.1 42690 1btl 263 2.09e+00 1btl e.3.1.1 42691 1tcvA 287 2.09e+00 1szwA 379 2.18e+00 d.265.1.4 99047 1m40A 263 2.33e+00 e.3.1.1 74437 1w19A 160 2.41e+00 1vybA 238 2.62e+00 d.151.1.1 108897 1k9sA 237 2.71e+00 c.56.2.1 68359 1tvxA 75 2.82e+00 1tvxA d.9.1.1 37441 6paxA 133 3.19e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1cl8A 276 3.46e+00 1ckqA c.52.1.1 33230 2ex4A 241 3.47e+00 2booA 247 3.53e+00 1dkzA 219 3.55e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 1c4kA 730 3.59e+00 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1jhdA 396 3.89e+00 b.122.1.3,c.26.1.5 66712,66713 2ghpA 292 3.95e+00 1d5rA 324 3.98e+00 1d5rA b.7.1.1,c.45.1.1 23181,32697 1k3eA 156 4.12e+00 d.198.1.1 68103 1nw1A 429 4.24e+00 d.144.1.8 86286 1ohtA 215 4.55e+00 d.118.1.1 87036 1j98A 157 4.72e+00 1j98A d.185.1.2 62755 1oz9A 150 4.88e+00 d.92.1.15 93808 1zczA 464 5.36e+00 1ve4A 206 5.51e+00 1bueA 265 5.83e+00 1btl e.3.1.1 42727 1yixA 265 6.21e+00 1mvwC 147 6.42e+00 i.15.1.1 79525 1eudB 396 6.71e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 1g6aA 271 6.80e+00 1btl e.3.1.1 42704 2b4yA 271 6.87e+00 2fp4B 395 7.05e+00 1o97D 320 7.18e+00 c.26.2.3,c.31.1.2 81233,81234 1sauA 115 7.23e+00 1wduA 245 7.47e+00 d.151.1.1 109286 2a07F 93 7.86e+00 1twdA 256 8.97e+00 c.1.30.1 107397 1b8aA 438 9.62e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1xubA 298 9.67e+00 1iuhA 198 9.92e+00 d.61.1.2 83711 1fm0E 150 1.02e+01 1fmaE d.41.5.1 38629 2comA 124 1.03e+01 1e5pA 151 1.04e+01 1bj7 b.60.1.1 59272 1f21A 155 1.05e+01 2rn2 c.55.3.1 33550 1xk4C 113 1.06e+01 1v2dA 381 1.09e+01 c.67.1.1 108281 1ntvA 152 1.09e+01 b.55.1.2 86168 1yal 218 1.10e+01 1cs8A d.3.1.1 37025 1e8gA 560 1.12e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1qgoA 264 1.13e+01 1qgoA c.92.1.2 35596 1y2qA 143 1.13e+01 1b8oA 284 1.15e+01 1b8oA c.56.2.1 33762 2rn2 155 1.17e+01 2rn2 c.55.3.1 33551 1t6kA 278 1.19e+01 1gz2A 142 1.20e+01 d.169.1.1 83392 1ifqA 138 1.24e+01 1ifqA d.110.4.1 62350 1b6rA 355 1.27e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1e25A 282 1.28e+01 1e25A e.3.1.1 42731 1fp1D 372 1.30e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1ji8A 111 1.31e+01 d.203.1.1 66733 1u1wA 298 1.31e+01 2cxxA 190 1.32e+01 2gdnA 267 1.38e+01 1kveB 77 1.38e+01 1kveB 2gk9A 426 1.41e+01 2cwcA 303 1.42e+01 1e7uA 961 1.42e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2c3mA 1231 1.55e+01 1o6dA 163 1.57e+01 c.116.1.3 92567 1jl1A 155 1.57e+01 c.55.3.1 66821 1atlA 202 1.59e+01 1atlA d.92.1.9 40322 1z7mA 344 1.63e+01 1w1kA 560 1.65e+01 d.58.32.1,d.145.1.1 109059,109060 2fyxA 143 1.70e+01 2liv 344 1.71e+01 2liv c.93.1.1 35708 1dzkA 157 1.71e+01 1obpA b.60.1.1 27096 1qg7A 67 1.71e+01 1a15A d.9.1.1 37449 1kekA 1231 1.76e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1e8yA 966 1.80e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2a6mA 155 1.82e+01 1vns 609 1.82e+01 1vns a.111.1.3 19061 1chuA 540 1.82e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ppjE 196 1.84e+01 b.33.1.1,f.23.12.1 104260,104261 1s1eA 224 1.85e+01 2f02A 323 1.85e+01 1yuwA 554 1.87e+01 1b0pA 1231 1.90e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 2b06A 155 1.92e+01 1rzhH 260 1.92e+01 b.41.1.1,f.23.10.1 98162,98163 1n3gA 113 1.93e+01 d.204.1.1 79962 1uwvA 433 1.94e+01 b.40.4.12,c.66.1.40 100128,100129 2awdA 323 1.97e+01 1o7eA 276 1.99e+01 e.3.1.1 92622 1yljA 263 2.00e+01 2gmqA 118 2.01e+01 1k4mA 213 2.01e+01 c.26.1.3 77258 1m98A 317 2.02e+01 a.175.1.1,d.17.4.6 78866,78867 1sqiA 393 2.05e+01 d.32.1.3,d.32.1.3 105914,105915 1e4fT 419 2.06e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 2gokA 429 2.06e+01 1j7lA 264 2.09e+01 d.144.1.6 62697 1top 162 2.10e+01 1ncx a.39.1.5 17223 1z15A 344 2.14e+01 1vhwA 253 2.16e+01 c.56.2.1 100706 1hzdA 272 2.16e+01 c.14.1.3 65969 1hzoA 271 2.18e+01 e.3.1.1 71092 1f46A 140 2.20e+01 1f46A d.129.4.1 59643 1q1gA 276 2.21e+01 c.56.2.1 95574 1jb3A 131 2.23e+01 1jc7A b.40.3.2 62833 1h2vC 771 2.24e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1txqA 93 2.26e+01 1n9bA 265 2.28e+01 e.3.1.1 85463 1gsoA 431 2.29e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2bdeA 470 2.30e+01 1h6kA 757 2.36e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1b5pA 385 2.38e+01 c.67.1.1 90403 1f3vA 179 2.40e+01 1f3vA d.58.22.1 39382 1omrA 201 2.50e+01 a.39.1.5 93349 1vhoA 346 2.56e+01 b.49.3.1,c.56.5.4 100694,100695 1r77A 103 2.59e+01 1jnyA 435 2.62e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1yacA 208 2.65e+01 1yacA c.33.1.3 31757 1zk7A 467 2.65e+01 1i2sA 282 2.65e+01 e.3.1.1 71104 1cjaA 342 2.68e+01 1cjaA d.144.1.3 41708 1ynpA 317 2.71e+01 2as0A 396 2.73e+01 1bza 262 2.76e+01 1btl e.3.1.1 42701 1d2zB 153 2.78e+01 1d2zB a.77.1.2 18439 1x31D 99 2.79e+01 1zbfA 142 2.84e+01 1e17A 150 2.84e+01 2hfh a.4.5.14 16143 1uyrA 737 2.88e+01 c.14.1.4,c.14.1.4 100188,100189 1q7zA 566 2.93e+01 c.1.21.2,c.1.26.1 96090,96091 7a3hA 303 2.93e+01 7a3hA c.1.8.3 28817 1zp4A 304 2.95e+01 1nu0A 138 2.98e+01 c.55.3.8 92165 1t0fA 276 3.02e+01 1gvjA 146 3.03e+01 a.4.5.21 90525 2fbmA 291 3.06e+01 1cfr 285 3.07e+01 1cfr c.52.1.7 33312 2cohA 202 3.10e+01 2ts1 419 3.21e+01 2ts1 c.26.1.1 31564 1l7aA 318 3.22e+01 c.69.1.25 77772 1u7kA 131 3.24e+01 1vd2A 89 3.26e+01 d.15.2.2 108517 1k78A 149 3.27e+01 a.4.1.5,a.4.1.5 68255,68256 1ky3A 182 3.28e+01 c.37.1.8 73193 1obpA 159 3.29e+01 1obpA b.60.1.1 27092 2d1sA 548 3.29e+01 1zb9A 143 3.30e+01 1qovH 260 3.32e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1ja1A 622 3.40e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1kcfA 258 3.41e+01 a.140.2.1,c.55.3.7 68434,68435 1xq6A 253 3.42e+01 1q4rA 112 3.49e+01 d.58.4.4 95823 1tikA 213 3.56e+01 c.23.5.3 107003 1oxcA 114 3.59e+01 b.115.1.1 93683 2fiuA 99 3.60e+01 1earA 147 3.61e+01 b.107.1.1,d.58.38.1 64875,64876 1ksoA 101 3.61e+01 a.39.1.2 72926 1vk0A 206 3.62e+01 c.55.3.5 100839 830cA 168 3.62e+01 1ck7A d.92.1.11 40400 1hqz1 141 3.64e+01 1j6oA 268 3.68e+01 c.1.9.12 77088 3kvt 115 3.73e+01 1t1dA d.42.1.2 38642 1rie 129 3.79e+01 1rie b.33.1.1 24427 1nm8A 616 3.82e+01 c.43.1.3,c.43.1.3 85872,85873 1gmmA 133 3.83e+01 b.18.1.10 65314 1t1uA 639 3.86e+01 1nnsA 326 3.86e+01 c.88.1.1 85910 2aqwA 332 3.88e+01 1vjpA 394 3.93e+01 c.2.1.3,d.81.1.3 100828,100829 1y13A 181 3.93e+01 1uzvA 114 3.95e+01 1uxxX 133 3.98e+01 b.18.1.10 100169 1gztA 115 3.98e+01 b.115.1.1 76428 3tdt 274 3.99e+01 3tdt b.81.1.2 28053 1bjwA 382 3.99e+01 1bjwA c.67.1.1 34349 1y7pA 223 4.02e+01 1lci 550 4.04e+01 1lci e.23.1.1 43349 1rpjA 288 4.09e+01 2dri c.93.1.1 35656 1usgA 346 4.09e+01 c.93.1.1 99864 2fy7A 287 4.10e+01 2lbp 346 4.14e+01 2liv c.93.1.1 35709 1b5tA 275 4.15e+01 1b5tA c.1.23.1 29676 1h3gA 601 4.15e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1iysA 262 4.16e+01 e.3.1.1 90723 1usmA 80 4.18e+01 d.74.1.1 99876 1rxyA 253 4.19e+01 c.56.2.1 98065 2ezh 75 4.25e+01 2ezh a.4.1.2 16029 1wab 232 4.30e+01 1wab c.23.10.3 31341 1aszB 490 4.31e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1on3A 523 4.35e+01 c.14.1.4,c.14.1.4 87107,87108 1es6A 296 4.39e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1lehA 364 4.41e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1qamA 244 4.42e+01 2ercA c.66.1.24 34220 1gvoA 364 4.45e+01 c.1.4.1 76357 1i76A 163 4.52e+01 1hfc d.92.1.11 61877 1a6f 119 4.53e+01 1a6f d.14.1.2 37564 1tif 78 4.54e+01 1tif d.15.8.1 37836 2ao0A 324 4.55e+01 1yp1A 202 4.55e+01 1vyrA 364 4.55e+01 c.1.4.1 108906 1h61A 364 4.55e+01 1oyc c.1.4.1 60657 1zq1A 438 4.59e+01 2fq3A 104 4.66e+01 1jilA 420 4.70e+01 c.26.1.1 66745 2etjA 250 4.79e+01 1w1wA 430 4.80e+01 1mg7A 417 4.80e+01 d.14.1.6,d.58.26.6 84954,84955 1zkeA 83 4.83e+01 1g8iA 190 4.89e+01 1rec a.39.1.5 60363 1bzyA 217 4.90e+01 1qk3A c.61.1.1 34071 1inlA 296 4.95e+01 c.66.1.17 66220 1qwyA 291 4.97e+01 b.84.3.2 96509 1amuA 563 4.97e+01 1amuA e.23.1.1 43351 1vhnA 318 4.97e+01 c.1.4.1 100693 1io2A 213 4.98e+01 1ekeA c.55.3.1 62612 1x42A 232 5.02e+01 1xpmA 396 5.03e+01 1o0xA 262 5.07e+01 d.127.1.1 80755 1ryaA 160 5.09e+01 d.113.1.5 105122 1ekfA 365 5.14e+01 1ekfA e.17.1.1 59445 1es9A 232 5.14e+01 1wab c.23.10.3 31340 1ku1A 230 5.17e+01 a.118.3.1 72996 1sxgA 280 5.17e+01 1whzA 70 5.18e+01 1bm9A 122 5.18e+01 1bm9A a.4.5.7 16116 1w1oA 534 5.18e+01 d.58.32.4,d.145.1.1 109071,109072 1v60A 123 5.21e+01 1st0A 337 5.21e+01 d.13.1.3,d.246.1.1 98979,98980 1ggzA 148 5.22e+01 a.39.1.5 70176 1x67A 146 5.30e+01 1uxaA 194 5.31e+01 b.21.1.1 108091 1guiA 155 5.31e+01 b.18.1.14 76351 2c6yA 111 5.36e+01 1lvaA 258 5.39e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1qnrA 344 5.41e+01 1qnoA c.1.8.3 28834 1vlbA 907 5.42e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1voqa 90 5.49e+01 2cruA 118 5.55e+01 1yzsA 121 5.55e+01 2bzlA 325 5.57e+01 1r89A 437 5.58e+01 a.160.1.3,d.218.1.7,d.58.16.2 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