# 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 1o0sA 605 8.76e-01 c.2.1.7,c.58.1.3 86540,86541 1fjrA 195 9.30e-01 1fjrA b.102.1.1 59855 1qg0A 308 1.24e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 1que 303 1.66e+00 1fnc b.43.4.2,c.25.1.1 25647,31537 2bsaA 303 1.80e+00 1rtfB 252 1.84e+00 5ptp 1go2A 304 1.91e+00 b.43.4.2,c.25.1.1 76243,76244 1qh0A 295 2.26e+00 b.43.4.2,c.25.1.1 68891,68892 1b2rA 304 2.36e+00 1fnc b.43.4.2,c.25.1.1 25648,31538 1fnd 314 2.52e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 2a9dA 372 2.62e+00 1ex7A 186 2.75e+00 1gky c.37.1.1 59537 1w34A 304 2.86e+00 1fnc 314 2.92e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1gky 187 2.95e+00 1gky c.37.1.1 31839 1fnb 314 3.05e+00 1fnc b.43.4.2,c.25.1.1 25628,31518 1ogiA 303 3.31e+00 b.43.4.2,c.25.1.1 92914,92915 1soxA 466 3.34e+00 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1bx1A 314 3.45e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1mwwA 128 3.46e+00 d.80.1.4 91483 1aokB 122 3.60e+00 1poa a.133.1.2 19561 1uch 230 3.78e+00 1uch d.3.1.6 37129 1pms 136 4.23e+00 1awe b.55.1.1 26966 1jltB 122 4.36e+00 a.133.1.2 66868 1ly1A 181 5.23e+00 c.37.1.1 74334 1xd3A 230 5.47e+00 1vj2A 126 5.63e+00 b.82.1.10 100796 1bb9 115 5.63e+00 1bb9 b.34.2.1 24554 1adwA 123 5.94e+00 1bqk b.6.1.1 22893 1dy9A 187 7.01e+00 1jxpA b.47.1.3 26400 1tu1A 148 7.08e+00 d.107.1.3 107316 1sxvA 172 7.16e+00 1ocxA 182 7.28e+00 b.81.1.3 86814 2b5oA 402 7.46e+00 1iz1A 294 7.68e+00 a.4.5.37,c.94.1.1 83823,83824 1ltqA 301 8.29e+00 c.108.1.9,c.37.1.1 78208,78209 1s31A 273 8.45e+00 1lst 239 8.76e+00 1lst c.94.1.1 35755 1d8hA 311 9.42e+00 1d8iA d.63.1.1 39544 2f1lA 187 9.60e+00 1dbhA 354 9.88e+00 1awe a.87.1.1,b.55.1.1 18514,26967 1ifrA 121 9.95e+00 b.1.16.1 71203 1aym3 238 1.01e+01 1aym3 1cjxA 357 1.02e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1c8zA 265 1.07e+01 1c8zA d.23.1.1 38375 1dkzA 219 1.13e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1gw0A 559 1.15e+01 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1b4aA 149 1.15e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1g55A 343 1.18e+01 1g55A c.66.1.26 34247 1b65A 375 1.20e+01 1b65A d.154.1.1 42020 3sil 379 1.21e+01 3sil b.68.1.1 27542 1d8iA 311 1.25e+01 1d8iA d.63.1.1 39541 1b3eA 330 1.26e+01 1nnt c.94.1.2 35897 1qpsA 261 1.27e+01 1ckqA c.52.1.1 33234 3nodB 423 1.28e+01 1nseA d.174.1.1 42513 1y8oB 128 1.30e+01 1uj6A 227 1.31e+01 c.124.1.4,d.58.40.1 107898,107899 1dtgA 334 1.34e+01 1nnt c.94.1.2 35896 2fmlA 273 1.35e+01 1qp8A 303 1.35e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1cp2A 269 1.38e+01 1cp2A c.37.1.10 32269 1i19A 561 1.39e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1dp4A 435 1.40e+01 1dp4A c.93.1.1 35710 1hxs3 237 1.44e+01 1pyaB 228 1.46e+01 1pyaB 1g2qA 187 1.52e+01 c.61.1.1 65117 2cyeA 133 1.53e+01 1t46A 313 1.53e+01 d.144.1.7 106397 1e79H 146 1.55e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1zj8A 566 1.56e+01 1dim 381 1.56e+01 3sil b.68.1.1 27544 1ywnA 316 1.59e+01 1dk4A 252 1.59e+01 1dk4A e.7.1.1 42970 1dkxA 219 1.63e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1a8e 329 1.71e+01 1cb6A c.94.1.2 35888 1vpqA 273 1.71e+01 1ryoA 327 1.76e+01 c.94.1.2 98108 1pvc3 238 1.77e+01 1aym3 2b18A 164 1.81e+01 1bpr 191 1.84e+01 1dkzA b.130.1.1 43319 1d3kA 329 1.85e+01 1nnt c.94.1.2 35889 1k1zA 78 1.88e+01 b.34.2.1 68026 1ckqA 276 1.92e+01 1ckqA c.52.1.1 33229 1g0hA 252 1.96e+01 1dk4A e.7.1.1 60171 2sil 381 2.07e+01 3sil b.68.1.1 27543 1y43B 173 2.11e+01 2aw5A 541 2.11e+01 1jqfA 334 2.13e+01 c.94.1.2 67086 2b6nA 278 2.14e+01 1kum 108 2.16e+01 1kum b.3.1.1 22525 1aj6 219 2.17e+01 1aj6 d.122.1.2 41106 2axyA 73 2.17e+01 1cl8A 276 2.19e+01 1ckqA c.52.1.1 33230 1jxcA 68 2.22e+01 g.3.7.5 77201 1ixcA 294 2.26e+01 a.4.5.37,c.94.1.1 83764,83765 1bawA 105 2.30e+01 1plc b.6.1.1 22868 1k4tA 592 2.32e+01 a.2.8.1,d.163.1.2,e.15.1.1 77263,77264,77265 2sxl 88 2.39e+01 1b7fA d.58.7.1 39179 1zbmA 280 2.43e+01 1fuiA 591 2.50e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1yemA 179 2.54e+01 1g8aA 227 2.55e+01 c.66.1.3 90506 1kdj 102 2.56e+01 1plc b.6.1.1 22864 1a31A 538 2.66e+01 1a36A d.163.1.2,e.15.1.1 42170,43263 1rlw 126 2.67e+01 1rlw b.7.1.1 23177 1fxoA 293 2.69e+01 1g0rA c.68.1.6 34524 1acz 108 2.73e+01 1kum b.3.1.1 22524 1b9wA 89 2.73e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2bkqA 212 2.74e+01 1lf2A 331 2.76e+01 b.50.1.2 77914 1x9gA 200 2.78e+01 c.33.1.3 109527 1h8eH 146 2.84e+01 1e79H b.93.1.1 60757 2f1rA 171 2.84e+01 1gdvA 85 2.85e+01 1ctj a.3.1.1 60458 1rliA 184 2.86e+01 c.23.5.6 97647 1gcqC 70 2.92e+01 1gcpA b.34.2.1 60436 1ac0 108 2.97e+01 1kum b.3.1.1 22526 1gq2A 555 3.01e+01 c.2.1.7,c.58.1.3 70308,70309 1tqnA 486 3.03e+01 a.104.1.1 107238 1ibvB 229 3.03e+01 1ak9 275 3.09e+01 1gci c.41.1.1 32517 1k6wA 426 3.11e+01 b.92.1.2,c.1.9.5 68236,68237 1sskA 158 3.14e+01 b.148.1.1 105986 1bcpC 199 3.14e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1mwmA 320 3.15e+01 c.55.1.1,c.55.1.1 79580,79581 1gppA 237 3.25e+01 b.86.1.2 76262 1ebfA 358 3.26e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1g0rA 293 3.28e+01 1g0rA c.68.1.6 34532 1ra0A 430 3.31e+01 2b1xA 470 3.31e+01 1to2E 281 3.35e+01 1a2q 275 3.36e+01 1gci c.41.1.1 32512 1j9jA 247 3.40e+01 c.106.1.1 62758 2eifA 136 3.46e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1cruA 454 3.50e+01 1c9uA b.68.2.1 27617 1h4rA 314 3.53e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1sup 275 3.55e+01 1gci c.41.1.1 32510 1dmhA 311 3.56e+01 1dmhA b.3.6.1 22633 1ze3D 125 3.60e+01 1v8fA 276 3.65e+01 c.26.1.4 100503 1mrzA 293 3.72e+01 b.43.5.1,c.26.1.3 91452,91453 1s21A 206 3.76e+01 d.166.1.4 105222 1xl3C 92 3.79e+01 1vk0A 206 3.84e+01 c.55.3.5 100839 1q41A 424 3.87e+01 d.144.1.7 95774 1aqn 275 3.89e+01 1gci c.41.1.1 32514 1twuA 139 3.90e+01 d.32.1.8 107413 1gcpA 70 3.95e+01 1gcpA b.34.2.1 60430 1a5iA 265 3.96e+01 5ptp b.47.1.2 26331 1jjhA 86 4.04e+01 2bopA d.58.8.1 63119 1gg3A 279 4.04e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1j9lA 247 4.05e+01 c.106.1.1 62762 1h59B 54 4.06e+01 g.3.9.1 70881 1kv9A 668 4.07e+01 a.3.1.6,b.70.1.1 73056,73057 1lw6E 281 4.07e+01 c.41.1.1 74293 1j1bA 420 4.10e+01 d.144.1.7 90758 1qxrA 189 4.12e+01 b.82.1.7 96552 2d4rA 147 4.23e+01 1eriA 276 4.26e+01 1ckqA c.52.1.1 33231 1qc9A 276 4.29e+01 1ckqA c.52.1.1 33235 1y4wA 518 4.36e+01 1rwiA 270 4.42e+01 b.68.9.1 97987 2ffcA 353 4.49e+01 1a35A 538 4.50e+01 1a36A d.163.1.2,e.15.1.1 42171,43264 1xkzA 255 4.53e+01 1dm9A 133 4.59e+01 1dm9A d.66.1.3 39560 1j5eE 161 4.61e+01 d.14.1.1,d.50.1.2 71547,71548 1rq2A 382 4.61e+01 c.32.1.1,d.79.2.1 105048,105049 2aaiB 262 4.66e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 2a90A 240 4.68e+01 1c9uA 454 4.70e+01 1c9uA b.68.2.1 27623 1nqeA 594 4.70e+01 f.4.3.3 86027 1sqeA 109 4.74e+01 d.58.4.5 105908 2blkA 122 4.77e+01 4rhv3 236 4.78e+01 1aym3 1wtaA 275 4.78e+01 2bjuA 453 4.78e+01 1jxpA 186 4.89e+01 1jxpA b.47.1.3 26402 2cz2A 223 4.90e+01 1ra9 159 4.92e+01 1vdrA c.71.1.1 34820 2bpsA 81 4.93e+01 1qbiA 454 4.93e+01 1c9uA b.68.2.1 27619 1dixA 208 5.00e+01 1bk7A d.124.1.1 41122 1fsu 492 5.19e+01 1auk c.76.1.2 35032 1ujnA 348 5.25e+01 e.22.1.1 99460 1ov3A 138 5.26e+01 b.34.2.1,b.34.2.1 87451,87452 3proC 166 5.33e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1xygD 359 5.36e+01 1t61A 229 5.39e+01 d.169.1.6,d.169.1.6 106529,106530 1pg6A 243 5.41e+01 b.82.5.2 94673 1fjgE 162 5.41e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1smeA 329 5.42e+01 1smrA b.50.1.2 26885 1yzfA 195 5.43e+01 1txvB 440 5.44e+01 1j1lA 290 5.44e+01 b.82.1.12 90766 1j3wA 163 5.45e+01 d.110.7.1 90833 1x82A 190 5.45e+01 1zd9A 188 5.46e+01 1jmcA 246 5.56e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1w85A 368 5.59e+01 2a5jA 191 5.63e+01 1wcqA 601 5.69e+01 1tvdA 116 5.69e+01 1tvdA b.1.1.1 20650 1ta9A 450 5.73e+01 1o59A 355 5.78e+01 b.18.1.22,b.18.1.22 92495,92496 2cc3A 150 5.78e+01 1wlpB 138 5.79e+01 1gdtA 183 5.81e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1k7kA 221 5.88e+01 c.51.4.1 72104 1pfzA 380 5.90e+01 1smrA b.50.1.2 26881 1xhbA 472 5.90e+01 1w8oA 601 5.90e+01 1vj0A 380 5.92e+01 b.35.1.2,c.2.1.1 100786,100787 1eljA 381 5.95e+01 4mbp c.94.1.1 35791 1cmoA 127 5.96e+01 1cmoA b.2.5.6 22462 1o4tA 133 5.97e+01 b.82.1.9 86622 1ik9A 213 6.05e+01 b.59.1.1,h.1.11.1 66176,66177 1cmxA 236 6.08e+01 1uch d.3.1.6 37130 1xg8A 111 6.12e+01 1res 43 6.14e+01 1ret a.4.1.2 16023 1xaoA 121 6.23e+01 1ignA 246 6.31e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 6dfr 159 6.33e+01 1vdrA c.71.1.1 34874 1mmvB 419 6.33e+01 d.174.1.1 91318 1crkA 380 6.35e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1a1rA 198 6.36e+01 1jxpA b.47.1.3 26406 1byuA 216 6.36e+01 1byuA c.37.1.8 32032 1om4A 422 6.43e+01 d.174.1.1 87067 1w2lA 99 6.43e+01 1xa1A 255 6.50e+01 e.3.1.1 109529 1mv3A 213 6.52e+01 b.34.2.1 91468 1kwkA 645 6.56e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1jiwI 106 6.66e+01 1smpI b.61.2.1 63078 1ti6B 274 6.66e+01 b.3.5.1,d.58.1.5 106976,106977 1k8hA 133 6.72e+01 b.111.1.1 72176 1u1zA 168 6.73e+01 d.38.1.6 107602 1sbzA 197 6.92e+01 1e19A 314 7.13e+01 1b7bA c.73.1.1 34967 1nnvA 110 7.14e+01 d.17.7.1 92012 1awe 130 7.14e+01 1awe b.55.1.1 26968 1a36A 592 7.16e+01 1a36A a.2.8.1,d.163.1.2,e.15.1.1 15715,42173,43266 1uj0A 62 7.16e+01 b.34.2.1 99449 3proD 166 7.18e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1xt9A 212 7.20e+01 1za7A 165 7.20e+01 2aegA 268 7.21e+01 1uteA 313 7.21e+01 1uteA d.159.1.1 42078 1k5cA 335 7.23e+01 b.80.1.3 72076 2avtA 378 7.27e+01 1yn4A 99 7.28e+01 1o0iA 138 7.33e+01 d.38.1.5 86532 1f5mB 180 7.37e+01 1f5mB d.110.2.1 40896 1dmzA 158 7.45e+01 1qu5A b.26.1.2 23921 1rjiA 31 7.46e+01 g.3.7.2 97568 2c0nA 203 7.46e+01 2biiA 424 7.54e+01 1wv9A 94 7.56e+01 1euu 605 7.57e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1qrjB 199 7.67e+01 1qrjB a.28.3.1 16952 1pxtB 390 7.70e+01 1afwA c.95.1.1,c.95.1.1 35906,35907 1fmb 104 7.71e+01 1fmb b.50.1.1 26777 1x92A 199 7.81e+01 1fyc 106 7.81e+01 1fyc b.84.1.1 28230 2bkrA 212 7.81e+01 1uunA 184 7.87e+01 f.6.1.2 100012 1wi9A 72 7.88e+01 1ryqA 69 7.92e+01 g.41.9.3 105126 1q9jA 422 7.94e+01 c.43.1.2,c.43.1.2 104590,104591 1wloA 136 7.97e+01 2f2eA 146 8.04e+01 1blxA 326 8.09e+01 1hcl d.144.1.7 41596 1yroB 286 8.20e+01 1ei1A 391 8.31e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1z8fA 228 8.34e+01 1qr6A 584 8.42e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 2udpA 338 8.42e+01 1xel c.2.1.2 29791 1plr 258 8.43e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1po5A 476 8.45e+01 a.104.1.1 94963 1s4iA 175 8.54e+01 1as4A 341 8.55e+01 1sek e.1.1.1 42623 1p9rA 418 8.58e+01 c.37.1.11 94399 1fgxA 288 8.63e+01 1fgxA c.68.1.2 34508 1b4eA 323 8.65e+01 1b4kA c.1.10.3 29186 1fadA 99 8.72e+01 1fadA a.77.1.2 18428 1ddsA 159 8.73e+01 1vdrA c.71.1.1 34858 1boeA 47 8.74e+01 1boeA g.3.9.1 44187 1i8jA 323 8.90e+01 1b4kA c.1.10.3 61968 1rybA 212 8.92e+01 c.56.3.1 98098 4dfrA 159 8.97e+01 1vdrA c.71.1.1 34822 2atvA 196 8.98e+01